@article {Stephens2005,
	title = {{Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.}},
	journal = {American journal of human genetics},
	volume = {76},
	number = {3},
	year = {2005},
	pages = {449{\textendash}62},
	abstract = {Although many algorithms exist for estimating haplotypes from genotype data, none of them take full account of both the decay of linkage disequilibrium (LD) with distance and the order and spacing of genotyped markers. Here, we describe an algorithm that does take these factors into account, using a flexible model for the decay of LD with distance that can handle both "blocklike" and "nonblocklike" patterns of LD. We compare the accuracy of this approach with a range of other available algorithms in three ways: for reconstruction of randomly paired, molecularly determined male X chromosome haplotypes; for reconstruction of haplotypes obtained from trios in an autosomal region; and for estimation of missing genotypes in 50 autosomal genes that have been completely resequenced in 24 African Americans and 23 individuals of European descent. For the autosomal data sets, our new approach clearly outperforms the best available methods, whereas its accuracy in inferring the X chromosome haplotypes is only slightly superior. For estimation of missing genotypes, our method performed slightly better when the two subsamples were combined than when they were analyzed separately, which illustrates its robustness to population stratification. Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site.},
	keywords = {Algorithms, Alleles, Biometry, Chromosomes, Data Interpretation, Genetic, Genomics, Genomics: statistics \& numerical data, Genotype, Haplotypes, Haplotypes: genetics, Human, Humans, Linkage Disequilibrium, Male, Models, Software, Statistical, X, X: genetics},
	issn = {0002-9297},
	doi = {10.1086/428594},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1196397\&tool=pmcentrez\&rendertype=abstract},
	author = {Stephens, Matthew and Scheet, Paul}
}
@article {Worheide2005,
	title = {{Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific}},
	journal = {Marine Biology},
	volume = {148},
	number = {5},
	year = {2005},
	month = {nov},
	pages = {907{\textendash}912},
	issn = {0025-3162},
	doi = {10.1007/s00227-005-0134-y},
	url = {http://link.springer.com/10.1007/s00227-005-0134-y},
	author = {W{\"o}rheide, Gert}
}
@article {Worheide2005a,
	title = {{Biodiversity, molecular ecology and phylogeography of marine sponges: patterns, implications and outlooks.}},
	journal = {Integrative and comparative biology},
	volume = {45},
	number = {2},
	year = {2005},
	month = {apr},
	pages = {377{\textendash}85},
	abstract = {Marine sponges are an ecologically important and highly diverse component of marine benthic communities, found in all the world{\textquoteright}s oceans, at all depths. Although their commercial potential and evolutionary importance is increasingly recognized, many pivotal aspects of their basic biology remain enigmatic. Knowledge of historical biogeographic affinities and biodiversity patterns is rudimentary, and there are still few data about genetic variation among sponge populations and spatial patterns of this variation. Biodiversity analyses of tropical Australasian sponges revealed spatial trends not universally reflected in the distributions of other marine phyla within the Indo-West Pacific region. At smaller spatial scales sponges frequently form heterogeneous, spatially patchy assemblages, with some empirical evidence suggesting that environmental variables such as light and/or turbidity strongly contribute to local distributions. There are no apparent latitudinal diversity gradients at larger spatial scales but stochastic processes, such as changing current patterns, the presence or absence of major carbonate platforms and historical biogeography, may determine modern day distributions. Studies on Caribbean oceanic reefs have revealed similar patterns, only weakly correlated with environmental factors. However, several questions remain where molecular approaches promise great potential, e.g., concerning connectivity and biogeographic relationships. Studies to date have helped to reveal that sponge populations are genetically highly structured and that historical processes might play an important role in determining such structure. Increasingly sophisticated molecular tools are now being applied, with results contributing significantly to a better understanding of poriferan microevolutionary processes and molecular ecology.},
	issn = {1540-7063},
	doi = {10.1093/icb/45.2.377},
	url = {http://icb.oxfordjournals.org/content/45/2/377},
	author = {W{\"o}rheide, Gert and Sol{\'e}-Cava, Antonio M and Hooper, John N A}
}
