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Fig. 1 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 1. Sampling sites and haplotypes found in and around the Carpathian Basin. Sam- ples collected in this study are marked with circles and haplotype codes, and previously

Fig. 5 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 5. Original drawings by O. Gy. Dely: male (A, B) and female (C, D) Ichthyosaura alpestris alpestris head shape from dorsal (A, C) and lateral (B, D) view

Fig. 4 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 4. Holotype of Triturus (=Ichthyosaura) alpestris bakonyiensis (Dely, 1964) (HNHM- HER-61.27.1.) from dorsal (A), lateral (B) and ventral (C) view

Fig. 8 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 8. Original drawings by O. Gy. Dely: female (A–D) and male (E–H) Ichthyosaura alpestris bakonyiensis skull from dorsal (A, E), ventral (B, F), lateral (C, G) and posterior (D, H) view

Fig. 7 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 7. Original drawings by O. Gy. Dely: female (A–D) and male (E–H) Ichthyosaura alpestris alpestris skull from dorsal (A, E), ventral (B, F), lateral (C, G) and posterior (D, H) view

Fig. 3 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 3. Median-joining network of the combined mtDNA haplotypes found in and around the Carpathian Basin (drawn with PopArt 1.7). Inset: distribution of Ichthyosaura alpestris in this region. On the network, circles with haplotype names mark haplotypes found in this

Fig. 6 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*

Fig. 6. Original drawings by O. Gy. Dely: male (A, B) and female (C, D) Ichthyosaura alpestris bakonyiensis head shape from dorsal (A, C) and lateral (B, D) view

Fig. 4 in Variations in infection levels and parasite-induced mortality among sympatric cryptic lineages of native amphipods and a congeneric invasive species: Are native hosts always losing?

Fig. 4. Parasite abundance as a function of amphipod body size (used as a proxy for age) in each of the 8 amphipod MOTUs. The polynomial effect of body size on parasite abundance is modeled with a general mixed effect linear model with a Poisson distribution and a log link function. The y axis is in log scale for representation purposes. Body size is rescaled to initial values in the graph for representation purposes. Predicted curves are represented in plain black lines with their standard errors in dotted lines.

Fig. 2 in Variations in infection levels and parasite-induced mortality among sympatric cryptic lineages of native amphipods and a congeneric invasive species: Are native hosts always losing?

Fig. 2. Mean parasite prevalences (proportion of infected individuals in %) among amphipod populations/sampling sites and their bootstrapped 95% confidence intervals in the different MOTUs sampled and for the three acanthocephalan species, separately and overall (all three parasites grouped). Overall prevalences in MOTUs assigned different letters are significantly different at the 0.05 level.

Fig. 1 in Variations in infection levels and parasite-induced mortality among sympatric cryptic lineages of native amphipods and a congeneric invasive species: Are native hosts always losing?

Fig. 1. Genetic divergence levels (%) among MOTUs of the G. fossarum/G. pulex species complex found in our sampling sites/rivers. Gammarus roeseli was identified morphologically rather than genetically.

Fig. 3 in Variations in infection levels and parasite-induced mortality among sympatric cryptic lineages of native amphipods and a congeneric invasive species: Are native hosts always losing?

Fig. 3. Mean parasite abundances (mean number of acanthocephalan larvae per individual host) among amphipod populations/sampling sites and their bootstrapped 95% confidence intervals in the different MOTUs sampled and for the three acanthocephalan species, separately and overall (all three parasites grouped). Overall abundances in MOTUs assigned different letters are significantly different at the 0.05 level.

opencc-zeroFeb 2020View details →

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Cryptic and extensive hybridization between ancient lineages of American crows

Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centered in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.

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Cryptic and extensive hybridization between ancient lineages of American crows

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publicFeb 2020View details →

opencc-zeroDec 2018View details →

Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

opencc-zeroSep 2022View details →

The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)

Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and the key to understanding their true evolutionary process. The genetic differentiation of the northern and southern Izu lineages of the Japanese newt Cynops pyrrhogaster was investigated through their single nucleotide polymorphism variations by multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto, and S-Kanto) those not detected by mtDNA in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The western populations of N-Kanto are close to S-Kanto, whereas the eastern populations of N-Kanto are close to Tohoku. Tohoku, N-Kanto, and S-Kanto are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history by the Approximate Bayesian Computation approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of the climatic oscillation in the Pleistocene. We concluded that the mitochondrial genome of S-Kanto was captured into Tohoku and the past original mitochondrial genome of Tohoku was entirely swept out from Tohoku through the hybridization.

publicNov 2024View details →

Holobiont traits shape climate change responses in cryptic coral lineages

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publicSep 2022View details →

The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)

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publicApr 2019View details →

Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

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