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opencc-zeroMay 2022View details →

Hybridization and low genetic diversity in the endangered Alabama Red-Bellied Turtle (Pseudemys alabamensis)

Pseudemys alabamensis is one of the most endangered freshwater turtle species in the United States due to its restricted geographic distribution in coastal Alabama and Mississippi. Populations of P. alabamensis are geographically isolated from one another by land and salt water, which could act as barriers to gene flow. It is currently unknown how differentiated these isolated populations are from one another and whether they have experienced reductions in population size. Previous work found morphological differences between Alabama and Mississippi populations, suggesting that they may be evolutionarily distinct. Other Pseudemys turtles such as P. concinna and P. floridana occur naturally within the same geographic area as P. alabamensis and are known to hybridize with each other. These more abundant species could threaten the unique genetic identity of P. alabamensis through introgression. In order to evaluate the endangered status of P. alabamensis and the level of hybridization with other species, we used mitochondrial and nuclear microsatellite markers to assess genetic variation within and among populations of P. alabamensis throughout its range and estimate admixture with co-occurring Pseudemys species. In P. alabamensis, we found no variation in mitochondrial DNA and observed an excess of homozygosity in the microsatellite data. Our results indicate evidence of genetic differentiation between Alabama and Mississippi populations of P. alabamensis, and low estimated breeding sizes and inbreeding for two populations (Fowl River, Alabama and Biloxi, Mississippi). Our results also support admixture of P. alabamensis with P. concinna/P. floridana. Based on our results, P. alabamensis is highly endangered throughout its range and threatened by both low population sizes and hybridization. In order to improve the species' chances of survival, focus should be placed on habitat preservation, maintenance of genetic diversity within both Mississippi and Alabama populations, and regular population monitoring activities such as nest surveillance and estimates of recruitment.

opencc-zeroMay 2022View details →

Phylogeny and evolution of Cupressaceae: updates on intergeneric relationships and new insights on ancient intergeneric hybridization

After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the <a name="_Hlk103290964"></a>vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.

opencc-zeroMay 2022View details →

Genotype data for: Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex

Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.

opencc-zeroDec 2021View details →

Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection

In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis only in limnetic crosses and breakdown in neither ecotype, suggesting that hybrid incompatibilities are environment-dependent for both ecotypes and that heterosis is environment-dependent in benthic crosses. Heterosis and breakdown were 3× greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, we observed qualitatively similar patterns of heterosis and hybrid breakdown in benthic crosses and limnetic crosses when averaging the lake pairs, suggesting that the outcome of hybridization is repeatable in a general sense.

opencc-by-4.0Jun 2022View details →

Verifying the Conformance of Human Behavior Using Hybrid Models - Synthetic Event Logs

Synthetic event logs used in the evaluation of the approach for the verification of conformance checking of human behavior, using hybrid process models.

opennotspecifiedMar 2013View details →

Distribution. NE Madagascar from the Bemarivo River, near Sambava, S to the region of Mananara-Nord, including the Masoala Peninsula and possibly extending from Marojejy W into Tsaratanana; there are additional isolated and most likely introduced populations in the Betampona Strict Nature Reserve and on Nosy Mangabe and on Ile Roger (also called Aye-aye I) near the town of Mananara-Nord. The distribution S of Mananara needs to be clarified because significant hybridization with the Brown Lemur (FE. fulvus) occurs over a wide area. in Lemuridae

Distribution. NE Madagascar from the Bemarivo River, near Sambava, S to the region of Mananara-Nord, including the Masoala Peninsula and possibly extending from Marojejy W into Tsaratanana; there are additional isolated and most likely introduced populations in the Betampona Strict Nature Reserve and on Nosy Mangabe and on Ile Roger (also called Aye-aye I) near the town of Mananara-Nord. The distribution S of Mananara needs to be clarified because significant hybridization with the Brown Lemur (FE. fulvus) occurs over a wide area.

opennotspecifiedMar 2013View details →

Distribution. SE coastal Madagascar, it occurs from Mandena Conservation Zone and the vicinity of Andohahela National Park, extending N, but how far is not known; it is not known where the hybrid zone begins and ends. in Lemuridae

Distribution. SE coastal Madagascar, it occurs from Mandena Conservation Zone and the vicinity of Andohahela National Park, extending N, but how far is not known; it is not known where the hybrid zone begins and ends.

opennotspecifiedJun 2022View details →

FIGURE 1 in Carex ×favratii (Cyperaceae), new record for Romania and evidence of its hybrid origin

FIGURE 1. PCoA plots depicting genotype differentiation between putative hybrid and parental species samples. Left: AFLP data, right: SSR (microsatellite) data. Legend: Carex echinata (asterisk), C. ×favratii (circle), C. paniculata (triangle).

opennotspecifiedJun 2015View details →

Distribution. NE Queensland from Mitchell River and near Mt Carbine (where it forms a hybrid zone with Godman's Rock Wallaby, P. godmani) W to Mungana and Undara, S to Burdekin River; W limit uncertain. in Macropodidae

Distribution. NE Queensland from Mitchell River and near Mt Carbine (where it forms a hybrid zone with Godman's Rock Wallaby, P. godmani) W to Mungana and Undara, S to Burdekin River; W limit uncertain.

opennotspecifiedJun 2015View details →

Distribution. SE Queensland from Fitzroy River S to Nanango (where it forms hybrid zone with the Brush-tailed Rock Wallaby, P. penicillata) and W to beyond Rubyvale and Clermont; W limit uncertain. in Macropodidae

Distribution. SE Queensland from Fitzroy River S to Nanango (where it forms hybrid zone with the Brush-tailed Rock Wallaby, P. penicillata) and W to beyond Rubyvale and Clermont; W limit uncertain.

opennotspecifiedJun 2015View details →

Distribution. NE Queensland from Mitchell River and near Mt Carbine (where it forms a hybrid zone with the Mareeba Rock Wallaby, P. mareeba) W to "Pinnacles" and N to Bathurst Head; W and N limits uncertain. in Macropodidae

Distribution. NE Queensland from Mitchell River and near Mt Carbine (where it forms a hybrid zone with the Mareeba Rock Wallaby, P. mareeba) W to "Pinnacles" and N to Bathurst Head; W and N limits uncertain.

opencc-zeroJun 2022View details →

Hybridization underlies localized trait evolution in cavefish

A rapidly growing body of work has demonstrated that introgressive hybridization often drives patterns of phenotypic evolution and may play an integral role in the evolutionary processes of local adaptation and speciation. Indeed, several of studies have shown that behavioral variation can result from introgressive hybridization (e.g., song in hybrid Darwin's finches, mate choice in hybrid baboons, defensive behavior in hybrid honey bees), providing new substrate for selection to act upon. A powerful model system for investigating the genetic and evolutionary basis of trait development and behavior is the Mexican tetra, Astyanax mexicanus. Cave populations have repeatedly evolved numerous traits including eye loss, sleep loss, and albinism. Of the 30 caves inhabited by A. mexicanus, the Chica cave is unique because it contains several pool microenvironments inhabited by putative hybrids between surface and cave populations, providing an opportunity to investigate hybridization and its impact on complex trait evolution. We demonstrate that hybridization between cave and surface populations contributes to highly localized variation in pigmentation, eye development, and sleep, traits that are thought to be associated with cave evolution. Our findings suggest that hybridization drives highly-localized behavioral and morphological evolution. Lastly, our analyses uncovered a compelling example of convergent evolution in a core circadian clock gene in multiple independent cavefish lineages and burrowing mammals, suggesting a shared genetic mechanism underlying circadian disruption in subterranean vertebrates. Together, our results provide insight into the evolutionary mechanisms that generate adaptive genetic variation.

opencc-zeroDec 2017View details →

Data from: Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

Elucidating the dynamic distribution of organismal lineages has been central to biology since the nineteenth century, yet the difficulty of combining biogeographic methods with shifts in habitat suitability remains a limitation. This integration, however, is critical to understanding geographic distributions, present and past, as well as the time-extended trajectories of lineages. Here, we link previous advances in phyloclimatic modeling to develop a framework that overcomes existing methodological gaps by predicting potential ecological and geographic overlap directly from estimated ancestral trait distributions. We show the utility of this framework by focusing on a clade in the montane angiosperm genus Heuchera, which is noteworthy in that it experienced ancient introgression from circumboreally distributed species of Mitella, lineages now ~1,300 km disjunct. Using this system, we demonstrate an application of ancestral state reconstruction to assess geographic range dynamics in a lineage lacking a fossil record. We test hypotheses regarding inferred past geographic distributions and examine the potential for ancient geographic contact. Application of this multifaceted approach suggests potential past contact between species of Heuchera and Mitella in western North America during cooler periods of the Pleistocene. Integration of niche models and phylogenetic estimates suggests that climatic cooling may have promoted range contact and gene flow between currently highly disjunct species. Our approach has wide applicability for testing hypotheses concerning organismal co-occurrences in deep time.

opennotspecifiedJul 2022View details →

FIGURE. Natural hybrids of Drosera sect. Drosera in Brazil. Drosera cayennensis × D. hirtella: a, rosette with emerging inflorescence (Cristalina, GO). Drosera communis × D. hirtella: b, rosette with emerging inflorescence (Parque Nacional da Chapada dos Veadeiros, GO). Drosera communis × D. lutescens: c, rosette with emerging inflorescence (Parque Nacional da Chapada dos Guimarães, MT). Drosera hirtella × D. lutescens (d, e): comparison between the hybrid (center) and the two parental species, D. hirtella (left) and D. lutescens (right); d, rosettes; e, scapes (Serra dos Pirineus, GO). Photo credits: a, b by PMG; c by Marcos Cardoso; d by FR. in A synopsis of the genus Drosera (Droseraceae) in Brazil

FIGURE. Natural hybrids of Drosera sect. Drosera in Brazil. Drosera cayennensis × D. hirtella: a, rosette with emerging inflorescence (Cristalina, GO). Drosera communis × D. hirtella: b, rosette with emerging inflorescence (Parque Nacional da Chapada dos Veadeiros, GO). Drosera communis × D. lutescens: c, rosette with emerging inflorescence (Parque Nacional da Chapada dos Guimarães, MT). Drosera hirtella × D. lutescens (d, e): comparison between the hybrid (center) and the two parental species, D. hirtella (left) and D. lutescens (right); d, rosettes; e, scapes (Serra dos Pirineus, GO). Photo credits: a, b by PMG; c by Marcos Cardoso; d by FR.

opencc-by-4.0Jul 2022View details →

Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact

Closely related taxa frequently exist in sympatry before the evolution of robust reproductive barriers, which can lead to substantial gene flow. Post-divergence gene flow can promote several disparate trajectories of divergence ranging from the erosion of distinctiveness and eventual collapse of the taxa to the strengthening of reproductive isolation. Among many relevant factors, understanding the demographic history of divergence (e.g. divergence time, extent of historical gene flow) can be particularly informative when examining contemporary gene flow between closely related taxa because this history can influence gene flow’s prevalence and consequences. Here, we used genotyping-by-sequencing data to investigate speciation and contemporary hybridization in two closely related and sympatrically distributed Lake Tanganyikan cichlid species in the genus Petrochromis. Demographic modeling supported a speciation scenario involving divergence in isolation followed by secondary contact with bidirectional gene flow. Further investigation of this recent gene flow found evidence of ongoing hybridization between the species that varied in extent between different co-occurring populations. Relationships between abundance and the degree of admixture across populations suggest that the availability of conspecific mates may influence patterns of hybridization. These results, together with the observation that sets of recently diverged cichlid taxa are generally geographically separated in the lake, suggest that ongoing speciation in Lake Tanganyikan cichlids relies on initial spatial isolation. Additionally, the spatial heterogeneity of admixture between the Petrochromis species illustrates the complexities of hybridization when species are in recent secondary contact.

FIGURE 5 in A new natural hybrid in Dionysia (Primulaceae)

FIGURE 5. Habitat of Dionysia diapensiifolia (a), and D. bryoides (b), D. diapensiifolia and D. bryoides co-occur in the same habitat (c).

FIGURE 4 in A new natural hybrid in Dionysia (Primulaceae)

FIGURE 4. Habitat of Dionysia × kowsarana and its parents. Yellow arrows: D. diapensiifolia, red: D. bryoides, white: Dionysia × kowsarana.

FIGURE 2 in A new natural hybrid in Dionysia (Primulaceae)

FIGURE 2. Flowers in D. diapensiifolia (a), Dionysia × kowsarana (c), D. bryoides (e). Leaves in D. diapensiifolia (b), Dionysia × kowsarana (d), D. bryoides (f).

FIGURE 3. Leaves. a in A new natural hybrid in Dionysia (Primulaceae)

FIGURE 3. Leaves. a, Dionysia × kowsarana: D-7045 (scale bar= 1 mm) b, D-7042 (scale bar= 1 mm) c, D-7043 (scale bar= 2 mm) d, D. bryoides (scale bar= 1 mm) e & f, D. diapensiifolia (scale bar= 2 mm). Marginal hairs of leaf: g, D. diapensiifolia h, hybrid i, D. bryoides (scale bar= 0.5 mm).

FIGURE 3 in A new hybrid of Origanum (Lamiaceae) from the Aegean Island of Karpathos (Dodecanese, Greece): Origanum × karpathicum

FIGURE 3 UPGMA cluster tree (a) and PCA diagram (b) realized on the systemic analysis of morphological data