The development of genetic tools to study populations at the molecular level has been one of the most important contributions to understand demographic processes in wild populations of conservation concern. Habitat loss and habitat fragmentation are the main factors causing declines of birds populations, as in the case of the Worthen’s sparrow (Spizella wortheni), a Mexican endemic Emberizid restricted to scrub and grassland habitats in northeastern Mexico. Here, I present the first molecular tools developed specifically for the study of S. wortheni populations. Genetic analyses of seven remnant populations of S. wortheni showed that no genetic impoverishment is present. This unexpected result may be caused by the nomadic life style of S. wortheni, which makes it tolerant to habitat modification. The high levels of inbreeding I found can be attributed to the tendency of S. wortheni to move in gregarious groups, since non-random mating might be present. My analyses based on the study of DNA segments from five mitochondrial genes support the hypotheses that S. wortheni and S. pusilla (Field Sparrow), as well as S. breweri (Brewer’s Sparrow) and S. passerina (Chipping Sparrow) are sister taxa. A phylogenetic network analysis showed that conflicting relationships among Spizella species might be caused by possible hybridization events between ancestors of extant taxa. Based on the study of the phylogenetic community structure, patterns of phylogenetic attraction and repulsion, and on the estimation of marginality, specialization and niche overlap among species, I investigated the possible causes of rarity in S. wortheni. The phylogenetic community structure analysis suggested that Spizella species are clustered across vegetation communities. Assuming phylogenetically conserved ecological traits, the phylogenetically clumped distribution may indicate habitat filtering among Spizella species. Additionally, behavioral traits such as flocking in mixed-species flocks might contribute to explain the pattern of community structure I found, and suggest that the rarity of S. wortheni is not a matter of interspecific competition. According to the phylogeny, evolutionary age was also discarded as a cause of rarity of this species. Compared with its congenerics, S. wortheni is the most specialized of all Spizella species. A potential evolutionary change of S. wortheni behavior that results in niche specialization is more likely to be the cause of its rarity.

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