Prospects for nuclear gene phylogeography

By Matthew P. Hare. 2001

388 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c55b8953dfff305bb05faf3d01450e5d15f976ba

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In Molecular Biology

Citations in the corpus

Molecular Studies and Phylogeography of Amazonian Tetrapods and their Relation to Geological and Climatic Models (2010, background): “Recent advances have incorporated nuclear genes (Hare 2001; Crawford 2003), but mtDNA remains the dominant marker, especially as few nuclear markers have suffi ciently rapid rates of evolution for intraspecifi c studies.”
What are fungal species and how to delineate them? (2021, neutral): “1980; Coyne and Orr 2004; Kohn 2005), and phylogeography (Avise 2000; Hare 2001; Kohn 2005).”
Perspective: conservation genetics enters the genomics era (2010, background): “Although some progress has been made (Hare 2001; Machado and Hey 2003), daunting hurdles remain, including the general technical challenge of isolating nuclear haplotypes from diploid specimens, and finding nuclear loci with relatively low levels of intra-genic recombination yet high levels of nucle”
The utility of single nucleotide polymorphisms in inferences of population history (2003, background): “that focus, for example, exclusively on INTRONS [ 3 ], we can envisage future studies in which SNP loci are sampled at random without reference to, or previous knowledge of, rates of mutation (Box 4). The least biased descriptions of genomic variation will come from studies that sample nucleotide si”
Comparative phylogeography of unglaciated eastern North America (2006, background): “Spisula solidissima surfclam mtDNA seq Atlantic Coast–Gulf Coast parsimony, 100% for each clade Hare & Weinberg (2005) Lampsilis sp.”
OPERATIONAL CRITERIA FOR DELIMITING SPECIES (2004, background): “The exclusivity criterion test requires sequences of unlinked gene regions that may not be available for many taxa, although this is changing (Hare 2001, Zhang & Hewitt 2003).”
Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects (2003, methodology): “These methods, in combination with coalescent analysis, appear to be able to overcome some of the major hurdles (such as multifurcation, recombination) of the traditional phylogenetic analysis techniques, and capable of recovering more precisely patterns of past population processes (Hare 2001).”
Contribution of genetics and genomics to seagrass biology and conservation (2007, background): “The advantage of genealogical approaches is that they link spatial history better than frequency-based methods and specifically allow for historical demographic estimates of past population bottlenecks and expansions based on tree shapes (Hare, 2001).”
Delimiting species: a Renaissance issue in systematic biology (2003, background): “requires multiple unlinked genetic markers, which are often not available for some taxa [ 55 ,56].”
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales (2002, background): “However, the number of phylogeographic analyses involving nuclear genes is increasing (Hare 2001).”
Land snails as a model to understand the role of history and selection in the origins of biodiversity (2002, background): “Unfortunately, working with nuclear gene sequences is technically more demanding, and the analysis requires further care, for reasons of the confusing effects of recombination (Hare 2001).”
Phylogeography: retrospect and prospect (2009, background): “Nonetheless, scnDNA haplotypes have been employed successfully in various phylogeographic assessments (Hare, 2001), with some of the most informative results coming from intron sequences at protein-coding genes.”