Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages

Jackson, Nathan D.; Austin, Christopher C.

doi:10.1111/j.1095-8312.2012.01929.x

Cited by 13 publications

(22 citation statements)

References 65 publications

(73 reference statements)

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“…Analyses with geographically selective sampling, where individuals would be sampled far from and in/near the contact zones, may be helpful to distinguish between the scenarios of divergence with gene flow and secondary contact, as the signal of gene flow could be reduced or eliminated when excluding particular individuals from or near contact zones (e.g. [40,45]). Our sampling of N. leucogenys and N. siki is limited and the provenances of these individuals are unclear.…”

Section: Resultsmentioning

confidence: 99%

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Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

et al. 2013

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BackgroundGibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus.ResultsTo investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki.ConclusionsOur multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera.

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Section: Resultsmentioning

confidence: 99%

“…In addition, multilocus data are suitable for the investigation of whether the divergence of closely related species was accompanied by gene flow (e.g. [39,40,42-51]).…”

Section: Introductionmentioning

confidence: 99%

Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

et al. 2013

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“…In selecting control sites, we ignored recent cutoffs that still retain residual connection to the main river because these have not yet likely released immigrants into the population [21]. Finally, we also sampled two sites far removed from the Mississippi River (Montgomery Co., AR and Benton Co., MS) referred to as “pure” sites which are assumed (based on previous mtDNA and nuclear sequence data [17], [18]) to exist away from the region of contact between groups separated by the river (Figure 3). …”

Section: Methodsmentioning

confidence: 99%

“…Despite this divergence in S. lateralis , there is some lineage overlap at sites close to the river, particularly near the river delta in southern Louisiana [17]. The boundary between two populations inferred using eight nuclear loci is characterized by even more extensive overlap than observed for mtDNA, and an isolation-with-migration model fits the multilocus data from these two populations better than an isolation-only model [18]. Thus, the Mississippi River appears to be acting as a “leaky barrier” for ground skink populations.…”

Section: Introductionmentioning

confidence: 93%

“…Broad scale genetic research on S. lateralis has revealed several genetic discontinuities that align with major southeastern rivers, suggesting that these rivers have historically isolated populations [17]. Despite this history of divergence, phylogeographic evidence suggests that some gene flow is occurring across rivers and thus that these riverine barriers may not be complete [18]. This is particularly true of the Mississippi River, one of the most cited dispersal barriers in the southeastern US [19].…”

Section: Introductionmentioning

confidence: 99%

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Testing the Role of Meander Cutoff in Promoting Gene Flow across a Riverine Barrier in Ground Skinks (Scincella lateralis)

Jackson

Austin

2013

PLoS ONE

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Despite considerable attention, the long-term impact of rivers on species diversification remains uncertain. Meander loop cutoff (MLC) is one river phenomenon that may compromise a river’s diversifying effects by passively transferring organisms from one side of the river to the other. However, the ability of MLC to promote gene flow across rivers has not been demonstrated empirically. Here, we test several predictions of MLC-mediated gene flow in populations of North American ground skinks (Scincella lateralis) separated by a well-established riverine barrier, the Mississippi River: 1) individuals collected from within meander cutoffs should be more closely related to individuals across the river than on the same side, 2) individuals within meander cutoffs should contain more immigrants than individuals away from meander cutoffs, 3) immigration rates estimated across the river should be highest in the direction of the cutoff event, and 4) the distribution of alleles native to one side of the river should be better predicted by the historical rather than current path of the river. To test these predictions we sampled 13 microsatellite loci and mitochondrial DNA from ground skinks collected near three ancient meander loops. These predictions were generally supported by genetic data, although support was stronger for mtDNA than for microsatellite data. Partial support for genetic divergence of samples within ancient meander loops also provides evidence for the MLC hypothesis. Although a role for MLC-mediated gene flow was supported here for ground skinks, the transient nature of river channels and morphologies may limit the long-term importance of MLC in stemming population divergence across major rivers.

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A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species

Wielstra

Baird

Arntzen

2013

Molecular Phylogenetics and Evolution

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The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species.

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Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages

Cited by 13 publications

References 65 publications

Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

Testing the Role of Meander Cutoff in Promoting Gene Flow across a Riverine Barrier in Ground Skinks (Scincella lateralis)

A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species

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