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
Introgression might be exceptionally common during the evolution of narrowly endemic species. For instance, in the springs of the small and isolated
- NSF-PAR ID:
- 10016328
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 6
- Issue:
- 11
- ISSN:
- 2045-7758
- Format(s):
- Medium: X Size: p. 3684-3698
- Size(s):
- ["p. 3684-3698"]
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract SNP s 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 twoSNP s in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non‐neutral nuclear clines were forSNP s in genes related to oxidative metabolism. Among these putatively non‐neutral nuclear clines,SNP s in two nuclear‐encoded mitochondrial genes (SLC 25A3 andHDDC 2), as well asSNP s in the myoglobin, 40S ribosomal protein S17, and actin‐bindingLIM 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. -
more » « less
Abstract The arrival to the
U nitedS tates of theA fricanized honey bee, a hybrid betweenE uropean subspecies and theA frican subspeciesA pis mellifera scutellataA frican andE uropean lineages in a feral population inS outhT exas. An 11‐year survey of this population (1991–2001) showed that mitochondrial haplotype frequencies changed drastically over time from a resident population of eastern and western European maternal ancestry, to a population dominated by theA frican haplotype. A subsequent study of the nuclear genome showed that theA fricanization process included bidirectional gene flow between European and Africanized honey bees, giving rise to a new panmictic mixture ofA . m. scutellata‐A. m. scutellata maternal ancestry, and three were of western European maternal ancestry. No colonies of eastern European maternal ancestry were detected, although they were present in the earlier samples. NuclearDNA revealed little change in the introgression ofA . m. scutellata -
more » « less
Abstract The Cyclophyllidea is the most diverse order of tapeworms, encompassing species that infect all classes of terrestrial tetrapods including humans and domesticated animals. Available phylogenetic reconstructions based either on morphology or molecular data lack the resolution to allow scientists to either propose a solid taxonomy or infer evolutionary associations. Molecular markers available for the Cyclophyllidea mostly include ribosomal
DNA and mitochondrial loci. In this study, we identified 3641 single‐copy nuclear coding loci by comparing the genomes ofHymenolepis microstoma ,Echinococcus granulosus andTaenia solium . We designedRNA baits based on the sequence ofH. microstoma , and applied target enrichment and Illumina sequencing to test the utility of those baits to recover loci useful for phylogenetic analyses. We capturedDNA from five species of tapeworms representing two families of cyclophyllideans. We obtained an average of 3284 (90%) of the targets from the test samples and then used captured sequences (2 181 361 bp in total; fragment size ranging from 301 to 6969 bp) to reconstruct a phylogeny for the five test species plus the three species for which genomic data are available. The results were consistent with the current consensus regarding cyclophyllidean relationships. To assess the potential for our method to yield informative genetic variation at intraspecific scales, we extracted 14 074 single nucleotide polymorphisms (SNP s) from alignments of fourArostrilepis macrocirrosa and twoA. cooki and successfully inferred their relationships. The results showed that our target gene tools yield data sets that provide robust inferences at a range of taxonomic scales in the Cyclophyllidea. -
more » « less
Abstract Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent
SNP s in a pair of sister morning glory species,Ipomoea cordatotriloba andI. lacunosa , are the result of divergent selection in the face of gene flow. We analysed aSNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater fromI. lacunosa toI. cordatotriloba than in the reverse direction, resulting in sympatric and allopatricI. cordatotriloba being substantially more different than sympatric and allopatricI. lacunosa . ManySNP s highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow,I. cordatotriloba traits become much more like those ofI. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation. -
more » « less
Abstract A major goal of invasion genetics is to determine how establishment histories shape non‐native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (
Gallus gallus ) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D‐loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancientDNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increasedG. gallus density on Kauai within the last few decades.SNP s obtained from whole‐genome sequencing were consistent with historic admixture between Kauai's divergent(G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feralG. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.
