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Statistical tests are needed to determine whether spatial structure has had a significant effect on the genetic differentiation of subpopulations. Here we introduce a new family of statistics based on a sum of an exponential function of the distances between individuals, which can be used with any genetic distance (e.g., nucleotide differences, number of nonshared alleles, or separation on a phylogenetic tree). The power of the tests to detect genetic differentiation in Wright-Fisher island models and stepping stone models was calculated for various sample sizes, rates of migration and mutation, and definitions of spatial neighborhoods. We found that our new test was in some cases more powerful than the Ks* statistic of Hudson et al. (Mol. Biol. Evol. 9, 138-151, 1992), but in all cases was slightly less powerful than both a traditional chi2 test without lumping of rare haplotypes and the S(nn) test of Hudson (Genetics 155, 2011-2014, 2000). However, when we applied our new tests to three data sets, we found in some cases highly significant results that were missed by the other tests.
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PMID:Exponential distance statistics to detect the effects of population subdivision. 1170 1

The number and location of Arctic glacial refugia utilized by taxa during the Pleistocene are continuing uncertainties in Holarctic phylogeography. Arctic grayling (Thymallus arcticus) are widely distributed in freshwaters from the eastern side of Hudson Bay (Canada) west to central Asia. We studied mitochondrial DNA (mtDNA) and microsatellite DNA variation in North American T. arcticus to test for genetic signatures of survival in, and postglacial dispersal from, multiple glacial refugia, and to assess their evolutionary affinities with Eurasian Thymallus. In samples from 32 localities, we resolved 12 mtDNA haplotypes belonging to three assemblages that differed from each other in sequence by between 0.75 and 2.13%: a 'South Beringia' lineage found from western Alaska to northern British Columbia, Canada; a 'North Beringia' lineage found on the north slope of Alaska, the lower Mackenzie River, and to eastern Saskatchewan; and a 'Nahanni' lineage confined to the Nahanni River area of the upper Mackenzie River drainage. Sequence analysis of a portion of the control region indicated monophyly of all North American T. arcticus and their probable origin from eastern Siberian T. arcticus at least 3 Mya. Arctic grayling sampled from 25 localities displayed low allelic diversity and expected heterozygosity (H(E)) across five microsatellite loci (means of 2.1 alleles and 0.27 H(E), respectively) and there were declines in these measures of genetic diversity with distance eastward from the lower Yukon River Valley. Assemblages defined by mtDNA divergences were less apparent at microsatellite loci, but again the Nahanni lineage was the most distinctive. Analysis of molecular variance indicated that between 24% (microsatellite DNA) and 81% (mtDNA) of the variance was attributable to differences among South Beringia, North Beringia and Nahanni lineages. Our data suggest that extant North American Arctic grayling are more diverse phylogeographically than previously suspected and that they consist of at least three major lineages that originated in distinct Pleistocene glacial refugia. T. arcticus probably originated and dispersed from Eurasia to North America in the late to mid-Pliocene, but our data also suggest more recent (mid-late Pleistocene) interactions between lineages across Beringia.
Mol Ecol 2004 Jun
PMID:Phylogeographical lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus. 1514 96

Watching ice floes glide by on the Hudson River from Eric Kandel's office, one gets a sense of placid reflection tempered by constant action-an apt analogy for Kandel's ability to calmly manage several ongoing projects and commitments at once. In addition to his well-lauded, ongoing research at Columbia University Medical Center's New York State Psychiatric Institute, Kandel has written several books on neurobiology, behavior, and memory. In addition to being a Nobel Laureate Scientist, he is well-known as an editor of the seminal textbook Principles of Neural Science. He and his colleagues are in the midst of working on a new edition of Principles, and he is working on a scientific autobiography. MI sat down with Dr. Kandel and discussed with him a range of topics including childhood and early career influences, intramural research at the NIH, the HHMI, ethical considerations of altering memory and, of course, Aplysia.
Mol Interv 2005 Apr
PMID:Eric Kandel: the future of memory. 1582 Nov 53

DNA sequences from five nuclear loci and data from three microsatellites were collected from 360 isolates representing 14 globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Haplotype networks were constructed for the five sequence loci and population subdivision was assessed using Hudson's permutation test. Migration estimates were calculated using six regional populations for both the sequence and microsatellite loci. While subdivision was detected among the six regional populations, significant gene flow was indicated among some of the populations. The European and Israeli populations contributed the majority of historical immigrants to the New World. Migration estimates for microsatellite loci were used to infer more recent migration events among specific New World populations. We conclude that gene flow was an important factor in determining the demographic history of Mycosphaerella graminicola.
Mol Ecol 2005 Jun
PMID:Migration patterns among global populations of the pathogenic fungus Mycosphaerella graminicola. 1591 Mar 13

Biological invasions may combine the genetic effects of population bottlenecks and selection and thus provide valuable insight into the role of such processes during novel environmental colonizations. However, these processes are also influenced by multiple invasions, the number of individuals introduced and the degree of similarity between source and receiving habitats. The amphipod Gammarus tigrinus provides a useful model to assess these factors, as its invasion history has involved major environmental transitions. This species is native to the northwest Atlantic Ocean, although it invaded both brackish and freshwater habitats in the British Isles after introduction more than 65 years ago. It has also spread to similar habitats in Western Europe and, most recently, to Eastern Europe, the Baltic Sea, and the Laurentian Great Lakes. To examine sources of invasion and patterns of genetic change, we sampled populations from 13 native estuaries and 19 invaded sites and sequenced 542 bp of the mitochondrial COI gene. Strong native phylogeographical structure allowed us to unambiguously identify three allopatrically evolved clades (2.3-3.1% divergent) in invading populations, indicative of multiple introductions. The most divergent clades occurred in the British Isles and mainland Europe and were sourced from the St Lawrence and Chesapeake/Delaware Bay estuaries. A third clade was found in the Great Lakes and sourced to the Hudson River estuary. Despite extensive sampling, G. tigrinus did not occur in freshwater at putative source sites. Some European populations showed reduced genetic diversity consistent with bottlenecks, although selection effects cannot be excluded. The habitat distribution of clades in Europe was congruent with the known invasion history of secondary spread from the British Isles. Differences in salinity tolerance among lineages were suggested by patterns of habitat colonization by different native COI clades. Populations consisting of admixtures of the two invading clades were found principally at recently invaded fresh and brackish water sites in Eastern Europe, and were characterized by higher genetic diversity than putative source populations. Further studies are required to determine if these represent novel genotypes. Our results confirm that biological invasions need not result in diminished genetic diversity, particularly if multiple source populations, each with distinctive genetic composition, contribute to the founding populations.
Mol Ecol 2006 Oct
PMID:Contrasting patterns in genetic diversity following multiple invasions of fresh and brackish waters. 1703 63

Analysis of population genetic relationships reveals the signatures of current processes such as spawning behaviour and migration, as well as those of historical events including vicariance and climate change. This study examines these signatures through testing broad- to fine-scale genetic patterns among smallmouth bass Micropterus dolomieu spawning populations across their native Great Lakes range and outgroup areas, with fine-scale concentration in Lake Erie. Our primary hypotheses include whether genetic patterns result from behavioural and/or geographical isolation, specifically: (i) Are spawning groups in interconnected waterways genetically separable? (ii) What is the degree of isolation across and among lakes, basins, and tributaries? (iii) Do genetic divergences correspond to geographical distances? and (iv) Are historical colonization patterns from glacial refugia retained? Variation at eight nuclear microsatellite DNA loci are analysed for 666 smallmouth bass from 28 locations, including 425 individuals in Lake Erie; as well as Lakes Superior, Huron, and Ontario, and outgroups from the Mississippi, Ohio, St. Lawrence, and Hudson River drainages. Results reveal marked genetic differences among lake and river populations, as well as surprisingly high divergences among closely spaced riverine sites. Results do not fit an isolation-by-geographical-distance prediction for fine-scale genetic patterns, but show weak correspondence across large geographical scales. Genetic relationships thus are consistent with hypotheses regarding divergent origins through vicariance in glacial refugia, followed by colonization pathways establishing modern-day Great Lakes populations, and maintenance through behavioural site fidelity. Conservation management practices thus should preserve genetic identity and unique characters among smallmouth bass populations.
Mol Ecol 2007 Apr
PMID:Broad- to fine-scale population genetic patterning in the smallmouth bass Micropterus dolomieu across the Laurentian Great Lakes and beyond: an interplay of behaviour and geography. 1740 77

Conspecific brood parasitism, where females of the same species lay eggs in each other's nests, is common in waterfowl, and is usually considered costly to host females, which are stuck looking after eggs and chicks that are not their own. However, since female waterfowl often exhibit an unusual propensity to nest near where they were born, there has been some uncertainty over whether, in ducks and geese, laying in nests of conspecifics really is parasitism. Do parasitic and host females tend to be related? And is parasitism actually a form of cooperation in disguise? In a population in Hudson Bay, Andersson & Waldeck (this issue) found that 'parasitic' eggs in nests of the common eider, Somateria mollissima sedentaria, are more closely related to host eggs than expected by chance. In fact, host and 'donor' eggs are more closely related than are females breeding at neighbouring nests. The Hudson Bay population of common eiders is unusual, because unlike in more benign climates, females do not tend to breed near their natal nest. Spatial proximity alone cannot account for the high relatedness between host eggs and 'dumped' or donor eggs. Instead, the high relatedness values are probably the result of active recognition, where females favour kin, either when dumping or accepting eggs. These new data, along with evidence indicating that the donor lays the first egg in the nest nearly half the time, suggest that what appears to be parasitism in common eiders may be a form of kin-based cooperation.
Mol Ecol 2007 Jul
PMID:Decoding dumping ducks. 1759 32

Conspecific brood parasitism (CBP), an alternative reproductive tactic where some females lay eggs in the nests of other females of the same species, occurs in many animals with egg care. It is particularly common in waterfowl, for reasons that are debated. Many waterfowl females nest near their birthplace, making it likely that some local females are relatives. We analyse brood parasitism in a Hudson Bay population of common eiders, testing predictions from two alternative hypotheses on the role of relatedness in CBP. Some models predict host-parasite relatedness, others predict that parasites avoid close relatives as hosts. To distinguish between the alternatives, we use a novel approach, where the relatedness of host-parasite pairs is tested against the spatial population trend in pairwise relatedness. We estimate parasitism, nest take-over and relatedness with protein fingerprinting and bandsharing analysis of egg albumen, nondestructively sampled from each new egg in the nest throughout the laying period. The results refute the hypothesis that parasites avoid laying eggs in the nests of related hosts, and corroborate the alternative of host-parasite relatedness. With an estimated r of 0.12-0.14, females laying eggs in the same nest are on average closer kin than nesting neighbour females. Absence of a population trend in female pairwise relatedness vs. distance implies that host-parasite relatedness is not only an effect of strong natal philopatry: some additional form of kin bias is also involved.
Mol Ecol 2007 Jul
PMID:Host-parasite kinship in a female-philopatric bird population: evidence from relatedness trend analysis. 1759 48

Phoxinus eos-neogaeus unisexual hybrids (Cyprinidae, Pisces) are among the few vertebrate taxa known to reproduce clonally by gynogenesis. These taxa have a broad distribution in North America, mostly located in regions previously covered by the last Pleistocene ice sheet. To assess whether asexual hybrids dispersed from glacial refuges at the end of the Pleistocene or they originated from current hybridization events, genetic diversity of mitochondrial DNA (mtDNA) sequences and microsatellite loci was determined in populations from 16 different sites in the Mississippi-Missouri River (Nebraska and Montana), Rainy River-Hudson Bay (Minnesota), and St Lawrence River (Quebec) drainages. The maternal species (P. neogaeus) occurred in Minnesota and Nebraska but was absent from Montana sites and was restricted to only two of 11 lakes sampled in Quebec, although hybrids were present at all sites. The genetic survey revealed a total of 49 clones, originating from 14 hybridization events. Several of the lineages were characterized by mtDNA haplotypes not detected in the maternal ancestor. Lineages as well as clones frequently displayed a large geographical distribution at a regional scale. Dating of hybridization events suggested a relatively recent origin (<50,000 years ago) from the Mississippi glacial refuge, even in regions not covered by the last Pleistocene glacier. Altogether, these results indicate P. eos-neogaeus hybrids are not the result of current hybridization events, but display a pattern predicted by postglacial dispersal. Our findings have considerable implications for the nature of selection processes affecting the diversity of these asexual taxa and their coexistence with sexual ancestors.
Mol Ecol 2007 Nov
PMID:The origin of Phoxinus eos-neogaeus unisexual hybrids. 1789 66

Trans-Arctic dispersals and population and range expansions during the Pleistocene enhanced opportunities for evolutionary diversification and contributed to the process of speciation within the capelin, a northern marine-fish complex exhibiting a circumpolar distribution. Capelin is composed of four highly divergent and geographically discrete mitochondrial DNA (mtDNA) clades (609 bp; cytochrome b). Two clades occur in the North Atlantic, one associated with Canadian Atlantic waters, including Hudson Bay, and the second distributed from West Greenland to the Barents Sea. Two additional clades occur in the Arctic and northeast Pacific Oceans, representing the most recent divergence within the capelin phylogenetic tree. Judged from mtDNA diversity, capelin populations comprising all clades experienced at least one demographic and spatial reduction-expansion episode during recent Pleistocene glaciations that imprinted their molecular architecture. The large contemporary populations in the northeast Pacific and Arctic Oceans exhibited significant genetic structure whereas no such structure was detected in the equally extensive North Atlantic clades. All clades are characterized by one or two prevalent mtDNA haplotypes distributed over the entire range of the clade. Assuming a Pacific ancestor for capelin, we infer that capelin dispersed on two separate occasions to the North Atlantic. A more recent event resulted in the isolation of eastern Pacific and Arctic clades, with the Arctic clade positioned for a potential third Atlantic invasion, as revealed by the presence of this clade in the Labrador Sea. The Labrador Sea is a potential contact zone for three of the four capelin clades.
Mol Ecol 2007 Dec
PMID:Trans-Arctic dispersals and the evolution of a circumpolar marine fish species complex, the capelin (Mallotus villosus). 1794 48


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