Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus)

Abstract

We investigated the phylogeography and subspecies classification of the ostrich (Struthio camelus) by assessing patterns of variation in mitochondrial DNA control region (mtDNA-CR) sequence and across fourteen nuclear microsatellite loci. The current consensus taxonomy of S. camelus names five subspecies based on morphology, geographic range, mtDNA restriction fragment length polymorphism and mtDNA-CR sequence analysis: S. c. camelus, S. c. syriacus, S. c. molybdephanes, S. c. massaicus and S. c. australis. We expanded a previous mtDNA dataset from 18 individual mtDNA-CR sequences to 123 sequences, including sequences from all five subspecies. Importantly, these additional sequences included 43 novel sequences of the red-necked ostrich, S. c. camelus, obtained from birds from Niger. Phylogeographic reconstruction of these sequences matches previous results, with three well-supported clades containing S. c. camelus/syriacus, S. c. molybdophanes, and S. c. massaicus/australis, respectively. The 14 microsatellite loci assessed for 119 individuals of four subspecies (all but S. c. syriacus) showed considerable variation, with an average of 13.4 (±2.0) alleles per locus and a mean observed heterozygosity of 55.7 (±5.3)%. These data revealed high levels of variation within most subspecies, and a structure analysis revealed strong separation between each of the four subspecies. The level of divergence across both marker types suggests the consideration of separate species status for S. c. molybdophanes, and perhaps also for S. c. camelus/syriacus. Both the mtDNA-CR and microsatellite analyzes also suggest that there has been no recent hybridization between the subspecies. These findings are of importance for management of the highly endangered red-necked subspecies (S. c. camelus) and may warrant its placement onto the IUCN red list of threatened animals.

Mitochondrial and Nuclear Genes-Based Phylogeography of Arvicanthis niloticus (Murinae) and Sub-Saharan Open Habitats Pleistocene History

“…Similar conclusions were also reached in plants (e.g., shea tree: [110]; giant lobelia: [111]; coffee tree: [112]), insects (e.g., maize stalk borer: [113]), reptiles (e.g., puff adder: [114]; Southern rock agama: [115]) and birds (e.g., starred robin: [116]; ostrich: [117]). Zoogeographic barriers to dispersal have also been pointed out in several species, including the Rift Valley (e.g., lion: [118]; giraffe: [100]; wildebeest: [102]; waterbuck: [105]; bushbuck: [107]; maize stalk borer: [113]; giant lobelia: [111]) and great rivers (e.g., [95]).…”

Stable Pleistocene-era populations ofChaerephon pumilus(Chiroptera: Molossidae) in southeastern Africa do not use different echolocation calls

“…lineages were established during the late Pleistocene, between 60 000 and 13 000 years ago. Consistent with this, Taylor et al (2009) suggested that two lineages (Clade 1.1 and 2.1 in our analyses) underwent population expansion 12 956-3 360 y BP and 59 434-14 726 y BP, respectively, possibly associated with expansion from Pleistocene glacial refugia, a process shown to be influential in shaping patterns of genetic diversification among different taxa (Matthee & Robinson 1997;Hewitt 2000;Flagstad et al 2001;Muwanika et al 2003;Hewitt 2004;Anthony et al 2007;Brown et al 2007;Voelker et al 2010;Miller et al 2011).…”

Profiling the Dead: Generating Microsatellite Data from Fossil Bones of Extinct Megafauna—Protocols, Problems, and Prospects

“…The value is comparable to, or perhaps slightly higher, than heterozygosity estimates of ostrich ( Struthio camelus ) subspecies (average H E ranged from 0.30 to 0.71), which appears to be the only other ratite that has been studied with microsatellite analyses [56]. The level of genetic diversity we recorded for Dinornis , combined with the discrimination power documented in the ‘Probability of Identity’ analysis, suggest that these six markers a highly informative and suitable for population genetic studies of moa.…”