Phylogeography and Pleistocene Evolution in the North American Black Bear

Wooding, S., and R. Ward. 1997. Mol. Biol. Evol 14:1096-1105.

Objectives: "to determine the character of phylogeographic structuring in a widespread North American carnivore" by 1) identifying if distinct patterns of distribution are present, 2) ascertaining the time scale over which diversity has evolved, using a molecular clock, 3a) identifying patterns of recent population growth using pairwise comparison of sequences, 3b) determining prevalance of migration by comparing geographic distributions of diversity and the context of lineage age, and 4) discussing patterns of genetic diversity with respect to geological and habitat changes

Methods:

• n=118 mtDNA sequences; Human primers H16498 and L15997, to amplify a control region in the mtDNA; Sequencing of single strand products

• n=258 RFLPS of bears from 16 localities; Clades identified in sequencing were used to identify diagnostic RFLPS so that future unsequenced samples could be assigned to clades by amplifying the human primers and digesting the PCR products with restriction enzymes

• Calculated a nucelotide substitution rate for the control region, using methods detailed by Waits 1996, resulting in 2.8% per Myr (slow for mammal coding)
• Used asiatic black bear as outgroup for phylogeographic analyses
• Population growth assessed with mismatch distributions for pairwise sequences, to see if sample evolved in a growing population (Rogers 1995).

Results and Conclusions:
"The long-term population history of black bears appears to be characterized predominantly by long-term regional isolation followed by recent contact and hybridization": two major clades were identified from 12 lineages and were spatially clustered, with one clade represented in 14/16 localities. The clades differed at an average of 4.8% of nucleotide positions, which is unusual within mammalian populations, and suggests deep/long-term divergence. The origin of black bear clades seem to have originated on the Pliocene/Pleistocene boundary, 1.6-2.0 MYA, with patterns in diversity congruent " with forest refuge formation during the Pleistocene and regional expansion based on expanding forest refugia.

Within regions, no obvious phylogeographic structuring is present, and that dispersal between populaton is probably a regular occurrence (may need to look at microsatellites to find any significant structure, which could also identify sex-biased differences since usats are biparentally inherited). Black bears have expanded with changes in their forest habitat, and patterns of genetic diversity within regions may be strongly affected by both regional mixing and population growth.

Keywords and Concepts:
 molecular phylogeography: " a means of understanding evolutionary processes within species" (Avise 1994), and for "understanding the historical factors leading to extant patterns of diversity",  using information from "geographical distrbution and topological relationships of genetic lineages, which reflects the long term structure and demographic history of populations"

mtdna:  mitochondrial DNA and is circular and double-stranded. It is only inherited maternally, and therefore has a smaller effective population size, and genetic drift can have a stronger effect. Has a higher mutation rate than nuclear DNA, and therefore can be used to track long ancestries

RFLPs: restriction fragment length polymorphism. fragmenting sequences of homologous DNA using restriction enzymes, and then separating the fragments by length.

Simulations suggest that lineage age  ∝  lineage range ( Neigel and Avise 1993)