New Insights into the Evolution of Intronic Sequences of the β-fibrinogen Gene and Their Application in Reconstructing Mustelid Phylogeny

Abstract

Mustelidae is the largest and most diverse family in the order Carnivora. The phylogenetic relationships among the subfamilies have especially long been a focus of study. Herein we are among the first to employ two new introns (4 and 7) of the nuclear β-fibrinogen gene to clarify these enigmatic problems. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) and one mt (ND2) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Detailed characterizations of the two intronic regions not only reveal the remarkable occurrences of short interspersed element (SINE) insertion events, providing a new example supporting the attractive hypothesis that attrition of an earlier retroposition may offer a proper environment for successive retropositions by forming a "dimer-like" structure, but also demonstrate their utility in the resolution of mustelid phylogeny. All of our analyses confirm the assemblage of Mustelinae, Lutrinae, and Melinae with confidence; moreover, two clades within Mustelinae were clearly recognized, i.e., genera Mustela and Martes. Notably, genus Martes of Mustelinae was found to branch off first, followed by Melinae and then a clade containing Lutrinae and genus Mustela of Mustelinae, indicating paraphyly of Mustelinae. In addition, Mephitinae diverges before the other mustelids and the monophyletic Procyonidae in all cases, supporting its elevation to a separate family. Additional independent genetic markers are still in need to resolve the trichotomy among Mephitinae and the other two carnivoran clades, Ailuridae and Procyonidae/non-mephitine Mustelidae.

Deciphering and dating the red panda’s ancestry and early adaptive radiation of Musteloidea

“…1). Most of the caniform interrelationships that have increasingly been hypothesized in recent molecular multilocus studies (Flynn et al, 2000Koepfli and Wayne, 2003;Sato et al, 2003Sato et al, , 2004Sato et al, , 2006Yu et al, 2004aYu et al, , 2008Delisle and Strobeck, 2005;Strobeck, 2006, 2007;Yu and Zhang, 2006;Árnason et al, 2007;Yonezawa et al, 2007;Koepfli et al, 2008;Wolsan and Sato, 2009), and that in part were also suggested by earlier research (e.g., Wolsan, 1993a;Dragoo and Honeycutt, 1997;Bininda-Emonds et al, 1999;and references therein), are here confirmed and extended. In particular, our multigene sequence data from protein-coding exons have provided compelling evidence for a sister relationship of the monophyletic pinnipeds to the musteloids, rather than ursids, and by that our diverse analyses substantially empower the most recent molecular resolution (Yu et al, 2004a;Sato et al, 2006;Fulton and Strobeck, 2006) of considerable long-standing controversy surrounding the relationships of pinnipeds (for a review of literature, see Sato et al, 2006).…”

“…In addition, as many as three out of their four topology tests failed to reject at P < 0.05 an alternative placement of the red panda relative to Mephitidae, and also their supertree analysis combining all individual gene ML trees placed the red panda in an unresolved trichotomy (with Mephitidae and a clade comprising Mustelidae and Procyonidae). All subsequent studies considering the phylogenetic arrangement hypothesized in Sato et al (2006) and Fulton and Strobeck (2006) have either found it as a poorly supported alternative to another, better supported, arrangement (Árnason et al, 2007;Fulton and Strobeck, 2007;Yu et al, 2008) or evaluated all competing arrangements as weakly supported (Yonezawa et al, 2007).…”

“…These have included placements in close affinity with ursids alone (e.g., Wozencraft, 1989) or ursids and pinnipeds (seals, sea lions, walruses; e.g., Vrana et al, 1994); among procyonids (e.g., Dragoo and Honeycutt, 1997); basally to a clade containing both ursids and procyonids as well as some other caniforms, including basal ones such as canids (dogs; e.g., Schreiber et al, 1998); or, at last, at or near the base of a clade comprising procyonids and mustelids (weasels, otters, martens, badgers, and their relatives). The last placement, initially postulated on the basis of chiefly fossil evidence (Schmidt-Kittler, 1981;Wolsan, 1993a), over recent years has repeatedly been recovered by phylogenetic analyses on combined molecular sequences from multiple loci, delivering unprecedented amounts of character data (Flynn and Nedbal, 1998;Flynn et al, 2000Yu et al, 2004aYu et al, , 2008Delisle and Strobeck, 2005;Strobeck, 2006, 2007;Sato et al, 2006;Yu and Zhang, 2006;Árnason et al, 2007;Peng et al, 2007;Yonezawa et al, 2007). Although confidence in a basal position of the red panda to the procyonid-mustelid clade has grown with increase in the genomic and taxonomic coverage of the sequence data, the persisting uncertainty about the relationship of the red panda to another living musteloid clade, the mephitids (skunks and stink badgers), has not been resolved decisively.…”

“…Although confidence in a basal position of the red panda to the procyonid-mustelid clade has grown with increase in the genomic and taxonomic coverage of the sequence data, the persisting uncertainty about the relationship of the red panda to another living musteloid clade, the mephitids (skunks and stink badgers), has not been resolved decisively. The mephitids themselves had long been viewed as mustelids based on fossil and other morphologic features (e.g., Schmidt-Kittler, 1981;Wozencraft, 1989;Wolsan, 1993aWolsan, , 1999Wyss and Flynn, 1993;Bininda-Emonds et al, 1999;Sato et al, 2004), but the overwhelming contradictory evidence that has accumulated from various genetic sources (Ledje and Árnason, 1996;Dragoo and Honeycutt, 1997;Flynn et al, 2000Sato et al, 2004Sato et al, , 2006Delisle and Strobeck, 2005;Strobeck, 2006, 2007;Árnason et al, 2007;Peng et al, 2007;Yonezawa et al, 2007;Yu et al, 2008; and references therein) persuasively argue for a position outside a clade containing mustelids and procyonids.…”

Evolutionary and biogeographic history of weasel-like carnivorans (Musteloidea)

“…Support for this relationship was, however, relatively weak. Most of the former multilocus molecular analyses have recovered the same phylogenetic arrangement between these two subfamilies Marmi et al, 2004;Fulton and Strobeck, 2006;Sato, 2006;Árnason et al, 2007;Schröder et al, 2009;Eizirik et al, 2010;Ki et al, 2010;Wolsan and Sato, 2010;Yamada and Masuda, 2010), whereas others placed Guloninae outside a clade containing Melinae and the morecrownward mustelids Yu and Zhang, 2006;Yu et al, 2008), hypothesized a sister relation between Melinae and Guloninae Yu et al, 2004;Fulton and Strobeck, 2006;Koepfli et al, 2008;Wolsan and Sato, 2010), or failed to resolve the relationship between the two subfamilies Fulton and Strobeck, 2006;Yu et al, 2008). The ferret-badgers (Melogale, Helictidinae) were strongly recovered as sister to a clade composed of Mustelinae, Ictonychinae, and Lutrinae (Figs.…”