Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus.

Bernardi, Giacomo; Sordino, P.; Powers, Dennis A.

doi:10.1073/pnas.90.20.9271

Cited by 85 publications

(64 citation statements)

References 19 publications

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“…This finding is consistent with previous work on this gene in F. heteroclitus , which has detected significant recombination within the Ldh‐B gene (Bernardi et al. 1993; Schulte et al. 1997).…”

Section: Resultsmentioning

confidence: 99%

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Steep, coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

McKenzie

Dhillon

Schulte

2016

Ecology and Evolution

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Steep genetic clines resulting from recent secondary contact between previously isolated taxa can either gradually erode over time or be stabilized by factors such as ecological selection or selection against hybrids. We used patterns of variation in 30 nuclear and two mitochondrial SNPs to examine the factors that could be involved in stabilizing clines across a hybrid zone between two subspecies of the Atlantic killifish, Fundulus heteroclitus. Increased heterozygote deficit and cytonuclear disequilibrium in populations near the center of the mtDNA cline suggest that some form of reproductive isolation such as assortative mating or selection against hybrids may be acting in this hybrid zone. However, only a small number of loci exhibited these signatures, suggesting locus‐specific, rather than genomewide, factors. Fourteen of the 32 loci surveyed had cline widths inconsistent with neutral expectations, with two SNPs in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non‐neutral nuclear clines were for SNPs in genes related to oxidative metabolism. Among these putatively non‐neutral nuclear clines, SNPs in two nuclear‐encoded mitochondrial genes (SLC25A3 and HDDC2), as well as SNPs in the myoglobin, 40S ribosomal protein S17, and actin‐binding LIM protein genes, had clines that were coincident and concordant with the mitochondrial clines. When hybrid index was calculated using this subset of loci, the frequency distribution of hybrid indices for a population located at the mtDNA cline center was non‐unimodal, suggesting selection against advanced‐generation hybrids, possibly due to effects on processes involved in oxidative metabolism.

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Section: Resultsmentioning

confidence: 99%

“…However, functional information regarding the genes containing these marker SNPs is still likely to be informative, because F. heteroclitus linkage groups appear to be small (Bernardi et al. 1993; Schulte et al. 1997), suggesting that the marker SNPs may be linked to functionally important SNPs within the same gene.…”

Section: Discussionmentioning

confidence: 99%

Steep, coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

McKenzie

Dhillon

Schulte

2016

Ecology and Evolution

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“…Bernardi et al, 1993). There were 14 polymorphic sites Northern Southern in hsp70-1, all of which were found in the southern population, whereas the sample from the northern populations exhibited no variation among individuals.…”

Section: Sequence Variation In Fundulus Hspsmentioning

confidence: 99%

Intraspecific variation in thermal tolerance and heat shock protein gene expression in common killifish,Fundulus heteroclitus

Fangue

Hofmeister

Schulte

2006

Journal of Experimental Biology

431

384

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SUMMARY Populations of common killifish, Fundulus heteroclitus, are distributed along the Atlantic coast of North America through a steep latitudinal thermal gradient. We examined intraspecific variation in whole-animal thermal tolerance and its relationship to the heat shock response in killifish from the northern and southern extremes of the species range. Critical thermal maxima were significantly higher in southern than in northern fish by ∼1.5°C at a wide range of acclimation temperatures (from 2-34°C), and critical thermal minima differed by ∼1.5°C at acclimation temperatures above 22°C, converging on the freezing point of brackish water at lower acclimation temperatures. To determine whether these differences in whole-organism thermal tolerance were reflected in differences in either the sequence or regulation of the heat shock protein genes(hsps) we obtained complete cDNA sequences for hsc70, hsp70-1 and hsp70-2, and partial sequences of hsp90α and hsp90β. There were no fixed differences in amino acid sequence between populations in either hsp70-1 or hsp70-2, and only a single conservative substitution between populations in hsc70. By contrast, there were significant differences between populations in the expression of many, but not all, of these genes. Both northern and southern killifish significantly increased hsp70-2 levels above control values(Ton) at a heat shock temperature of 33°C, but the magnitude of this induction was greater in northern fish, suggesting that northern fish may be more susceptible to thermal damage than are southern fish. In contrast, hsp70-1 mRNA levels increased gradually and to the same extent in response to heat shock in both populations. Hsc70 mRNA levels were significantly elevated by heat shock in southern fish, but not in northern fish. Similarly, the more thermotolerant southern killifish had a Ton for hsp90α of 30°C, 2°C lower than that of northern fish. This observation combined with the ability of southern killifish to upregulate hsc70 in response to heat shock suggests a possible role for these hsps in whole-organism differences in thermal tolerance. These data highlight the importance of considering the complexity of the heat shock response across multiple isoforms when attempting to make linkages to whole-organism traits such as thermal tolerance.

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“…8), has not yielded useful amounts population-level variation. An alternative source of variation, the noncoding regions of ''singlecopy'' (low copy number) nuclear genes, has not been extensively explored in plants (5,(9)(10)(11), although this genome can potentially provide multiple, unlinked allele genealogies at the intraspecific level (12)(13)(14).…”

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confidence: 99%

Evidence on the origin of cassava: Phylogeography of Manihot esculenta

Olsen

Schaal

1999

Proc. Natl. Acad. Sci. U.S.A.

437

299

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Cassava (Manihot esculenta subsp. esculenta) is a staple crop with great economic importance worldwide, yet its evolutionary and geographical origins have remained unresolved and controversial. We have investigated this crop's domestication in a phylogeographic study based on the single-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (G3pdh). The G3pdh locus provides high levels of noncoding sequence variation in cassava and its wild relatives, with 28 haplotypes identified among 212 individuals (424 alleles) examined. These data represent one of the first uses of a single-copy nuclear gene in a plant phylogeographic study and yield several important insights into cassava's evolutionary origin: (i) cassava was likely domesticated from wild M. esculenta populations along the southern border of the Amazon basin; (ii) the crop does not seem to be derived from several progenitor species, as previously proposed; and (iii) cassava does not share haplotypes with Manihot pruinosa, a closely related, potentially hybridizing species. These findings provide the clearest picture to date on cassava's origin. When considered in a genealogical context, relationships among the G3pdh haplotypes are incongruent with taxonomic boundaries, both within M. esculenta and at the interspecific level; this incongruence is probably a result of lineage sorting among these recently diverged taxa. Although phylogeographic studies in animals have provided many new evolutionary insights, application of phylogeography in plants has been hampered by difficulty in obtaining phylogenetically informative intraspecific variation. This study demonstrates that single-copy nuclear genes can provide a useful source of informative variation in plants.

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Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus.

Cited by 85 publications

References 19 publications

Steep, coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

Steep, coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

Intraspecific variation in thermal tolerance and heat shock protein gene expression in common killifish,Fundulus heteroclitus

Evidence on the origin of cassava: Phylogeography of Manihot esculenta

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