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opennotspecifiedSep 2019View details →

Figure 2 in Life in the thornscrub: movementı home rangeı and territoriality of the reticulate collared lizard (Crotaphytus reticulatus)

Figure 2. Example of telemetry harness attached to female reticulate collared lizard (Crotaphytus reticulatus) in typical Tamaulipan thornscrub habitat found in April 2017 on the East Foundation's San Antonio Viejo Ranch in Jim Hogg and northern Starr Counties, Texas, USA. (Photo credit: W. A. Ryberg).

opennotspecifiedSep 2019View details →

Figure 3 in Life in the thornscrub: movementı home rangeı and territoriality of the reticulate collared lizard (Crotaphytus reticulatus)

Figure 3. Box plots showing significant differences between log-transformed male and female reticulate collared lizard (Crotaphytus reticulatus) (a) Mean step length (m), (b) Minimum convex polygon (m2), (C) 95% kernel density estimation (m2), and (D) 50% kernel density estimation (m2). Movement parameters were estimated with GPS telemetry in Jim Hogg and Starr Counties, Texas (2015–17).

opencc-zeroJan 2021View details →

Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)

Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridisation and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridisation has previously been reported in the Australian endemic plant genus Adenanthos (Proteaceae). Like many Australian genera, Adenanthos is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for Adenanthos, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridisation and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also result from extensive ancient introgression as well as recent chloroplast capture and introgression between extant Adenanthos species. The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localised populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in Adenanthos coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly.

opencc-zeroDec 2013View details →

Data from: Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids

Reticulate evolution can be a major driver of diversification into new niches, especially in disturbed habitats and at the edges of ranges. Industrial fermentation strains of yeast provide a window into these processes, but progress has been hampered by a limited understanding of the natural diversity and distribution of Saccharomyces species and populations. For example, lager beer is brewed with Saccharomyces pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a species only recently discovered in Patagonia, Argentina. Here we report that genetically diverse strains of S. eubayanus are readily isolated from Patagonia, demonstrating that the species is well established there. Analyses of multi-locus sequence data strongly suggest that there are two diverse and highly differentiated Patagonian populations. S. eubayanus alleles present among hybrid European brewing strains had strikingly low diversity, suggesting they were drawn from a small subpopulation that is closely related to one of the Patagonian populations. For the first time, we also report the rare isolation of S. eubayanus outside of Patagonia, in Wisconsin, USA. In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. These complex and varied reticulation events are not adequately captured by conventional phylogenetic methods and required analyses of Bayesian concordance factors and phylogenetic networks to accurately summarize and interpret. These findings show how genetically diverse eukaryotic microbes can produce rare but economically important hybrids with low genetic diversity when they migrate from their natural ecological context.

opencc-zeroDec 2012View details →

Data from: Timeframes of speciation, reticulation, and hybridization in the Bulldog bat explained through phylogenetic analyses of all genetic transmission elements

Phylogenetic comparisons of the different mammalian genetic transmission elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for understanding the process of speciation in nature. Through such comparisons the unique inheritance pathways of each genetic element and gender-biased processes can link genomic structure to the evolutionary process, especially among lineages which have recently diversified, in which genetic isolation may be incomplete. Bulldog bats of the genus Noctilio are an exemplar lineage, being a young clade, widely distributed, and exhibiting unique feeding ecologies. In addition, currently recognized species are paraphyletic with respect to the mtDNA gene tree and contain morphologically identifiable clades that exhibit mtDNA divergences as great as among many species. To test taxonomic hypotheses and understand the contribution of hybridization to the extant distribution of genetic diversity in Noctilio, we used phylogenetic, coalescent stochastic modeling, and divergence time estimates using sequence data from cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as well as evolutionary reconstructions based on amplified fragment length polymorphisms (AFLP) data. No evidence of ongoing hybridization between the two currently recognized species was identified. However, signatures of an ancient mtDNA capture were recovered in which an mtDNA lineage of one species was captured early in the noctilionid radiation. Among subspecific mtDNA clades, which were generally coincident with morphology and statistically definable as species, signatures of ongoing hybridization were observed in sex chromosome sequences and AFLP. Divergence dating of genetic elements corroborates the diversification of extant Noctilio beginning about three million years ago, with ongoing hybridization between mitochondrial lineages separated by 2.5 million years. The time-frame of species' divergence within Noctilio supports the hypothesis that shifts in the dietary strategies of gleaning insects (N. albiventris) or fish (N. leporinus) are among the most rapid instances of dietary evolution observed in mammals. This study illustrates the complex evolutionary dynamics shaping gene pools in nature, how comparisons of genetic elements can serve for understanding species boundaries, and the complex considerations for accurate taxonomic assignment.

opencc-zeroDec 2016View details →

Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.

opencc-zeroDec 2012View details →

Data from: A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

Background: Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. Results: Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 -- 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 -- 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. Conclusions: Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

FIGURE 1 in A new Phyllomedusa Wagler (Anura, Hylidae) with reticulated pattern on flanks from Southeastern Brazil

FIGURE 1. Three closely related species of Phyllomedusa from the state of Minas Gerais in life. A and B– Phyllomedusa araguari sp. n. (A– holotype ZUEC 1280; B– paratopotype AAG-UFU 2576); C– Phyllomedusa megacephala, Serra do Cipó; D– Phyllomedusa ayeaye topotype. C and D– unvouchered photos.

FIGURE 5 in A new Phyllomedusa Wagler (Anura, Hylidae) with reticulated pattern on flanks from Southeastern Brazil

FIGURE 5. The advertisement call of Phyllomedusa megacephala. A– Spectrogram of an entire call with seven notes, B– Spectrogram, C– Oscillogram, and D– Power spectrum of the fifth note; a denotes the background call of other frog species (Physalaemus cuvieri). AAG sound file PhyllomedmegacepMG3AAGb. Specimen recorded on December 04 2005, 18:40 h; air 17.9, water 22.9 C. Voucher: AAG photo (Figure 1C). Specimen from Serra do Cipó, Minas Gerais, Brazil.

FIGURE 4 in A new Phyllomedusa Wagler (Anura, Hylidae) with reticulated pattern on flanks from Southeastern Brazil

FIGURE 4. The advertisement call of Phyllomedusa araguari sp. n.. A– Spectrogram of an entire call with nine notes, B– Spectrogram, C– Oscillogram, and D– Power spectrum of the fifth note. AAG sound file PhyllomedaraguMG1bAAGm. Specimen recorded on December 05 2003, 21:40 h; air temperature 23 C. Voucher paratopotype AAG-UFU 2597. Estação de Pesquisa e Desenvolvimento Ambiental Galheiro (CEMIG), municipality of Perdizes, Minas Gerais, Brazil.

FIGURE 3 in A new Phyllomedusa Wagler (Anura, Hylidae) with reticulated pattern on flanks from Southeastern Brazil

FIGURE 3. Dorsal views of three closely related species of Phyllomedusa illustrating their general aspect and patters on the hidden parts of legs. At right Phyllomedusa araguari sp. n. types (A and C– holotype ZUEC 12880 (former AAG- UFU 2598); B– paratopotype AAG-UFU 2576). Upper left– P. megacephala (ZUEC 2284), Serra do Cipó; Middle left– P. ayeaye (ZUEC 4160) topotype; Bottom left– P. o re a d e s (CHUNB 12515) topotype.

FIGURE 2 in A new Phyllomedusa Wagler (Anura, Hylidae) with reticulated pattern on flanks from Southeastern Brazil

FIGURE 2. Phyllomedusa araguari sp. n. (holotype AAG-UFU 12880). A– Dorsal and B– lateral views of head; C– palmar and D– plantar views.

opennotspecifiedDec 2014View details →

FIGURE 6. Porania pulvillus USNM E08391 P. pulvillus-Scotland. A. Abactinal surface. B. Actinal surface. C. USNM 5533 P. insignis Paralectotype showing densely arranged abactinal skeleton. D. USNM 6385 P. insignis Paralectotype showing widely arranged reticulate skeleton. E. USNM E46649 P in New taxa and taxonomic revisions to the Poraniidae (Valvatacea; Asteroidea) with Comments on Feeding Biology

FIGURE 6. Porania pulvillus USNM E08391 P. pulvillus-Scotland. A. Abactinal surface. B. Actinal surface. C. USNM 5533 P. insignis Paralectotype showing densely arranged abactinal skeleton. D. USNM 6385 P. insignis Paralectotype showing widely arranged reticulate skeleton. E. USNM E46649 P. pulvillus, Nova Scotia, showing denuded abactinals, superomarginals and inferomarginal series. F. Denuded densely arranged/imbricate abactinal plates.

FIGURE 3 in A new fossil species of the reticulated beetle genus Cupes (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber

FIGURE 3. Morphological details of Cupes balticus sp. n., holotype, SEHU-0000121237. A, Head with morphological interpretations, dorsal view. B, Head without morphological interpretations, dorsal view. C, Pronotum with morphological interpretations, dorsal view. C, Pronotum without morphological interpretations, dorsal view. Abbreviations: a1–2, antennomeres 1–2; ey, eyes; fs, paramedian fossae at anterior pronotal edge; fv, longitudinal median furrow on vertex; mrp, median elevated ridge of pronotum; p1, supraantennal tubercle; p2, supraocular tubercle; pn, pronotum; tmp, temple.

FIGURE 4 in A new fossil species of the reticulated beetle genus Cupes (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber

FIGURE 4. Morphological details of Cupes balticus sp. n., holotype, SEHU-0000121237. A, Head, right antenna, and prothorax, ventral view. B, Forelegs, ventral view. C, Basal part of left antenna, ventral view. D, Mid- and hindlegs, ventral view. E, Abdomen, ventral view. Abbreviations: a3–6, antennomeres 3–6; v1–5, ventrites 1–5. Scale bars: 1.0 mm (A–D); 2.0 mm (E).

FIGURE 1 in A new fossil species of the reticulated beetle genus Cupes (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber

FIGURE 1. General habitus of Cupes balticus sp. n., holotype, SEHU-0000121237. A, Dorsal view. B, Ventral view. Scale bars: 3.0 mm.

FIGURE 2 in A new fossil species of the reticulated beetle genus Cupes (Coleoptera: Archostemata: Cupedidae) from Eocene Baltic amber

FIGURE 2. Morphological details of Cupes balticus sp. n., holotype, SEHU-0000121237. A, Head and pronotum, dorsal view. B, Head, dorsal view. C, Right lateral half of pronotum, dorsal view. D, Left elytron and scutellum, dorsal view. E, Right metatarsus, dorsal view. F, Left antenna, dorsal view. Abbreviations: a1–11, antennomeres 1–11; ey, eyes; fv, longitudinal median furrow on vertex; mtt1–5, metatarsomeres 1–5; p1, supraantennal tubercle; p2, supraocular tubercle; tmp, temple. Scale bars: 1.0 mm (A); 0.5 mm (B, C, E); 2.0 mm (D, F).

opennotspecifiedOct 2022View details →

Fig. 6 in A phylogenetic investigation of the taxonomically problematic Eucalyptus odorata complex (E. section Adnataria series Subbuxeales): evidence for extensive interspecific gene flow and reticulate evolution

Fig. 6. Isolation by distance plot of core E. odorata complex samples (E. odorata, E. cajuputea, E. wimmerensis, E. walshii, E. yarriambiack, E. filiformis, E. polybractea and E. viridis from south-eastern Queensland). Geographic distances are kilometres between collection coordinates and genetic distances are uncorrelated-P distances.