Origin Of Lineages Research Articles

Limited dispersal and in situ diversification drive the evolutionary history of Rasborinae fishes in Sundaland

AbstractAimSea‐level changes have long been put forward to explain the colonization of Southeast Asian islands by freshwater aquatic organisms. We examined the relative impact of Sundaland geology since the Oligocene and of Pleistocene Eustatic Fluctuations on the mitochondrial lineage diversification of a species‐rich subfamily of freshwater fishes widely distributed in Southeast Asia. We specifically tested if the expansion of exposed lands and increased island connectivity during Pleistocene low sea levels (the paleoriver hypothesis) induced bursts of diversification.LocationSundaland.TaxonRasborinae (Actinopterygii, Cypriniformes, Danionidae).MethodsWe aggregated 1,017 cytochrome oxidase I sequences and 79 mitogenomes to delineate Molecular Operational Taxonomic Units (MOTUs) and further reconstruct a time‐calibrated phylogeny of Rasborinae. Ancestral area estimations were conducted using both island and paleoriver partitioning to examine the impact of island connectivity during Pleistocene sea‐level changes on dispersal. Temporal trends of diversification are explored through statistical selection of best‐fit models.ResultsThe origin of Sundaland mitochondrial lineages is dated at c. 33 Ma and four major clades are identified, which diversified between c. 31 and 22 Ma. The Island of Borneo and North Sunda paleoriver are identified as the source of Sundaland Rasborinae. Geographical patterns of lineage divergence indicate that most divergence events occurred within islands and diversification under constant birth rate models are the most likely for all clades.ConclusionsThe geographical and historical context of diversification of mitochondrial lineages in Rasborinae provides little support for the paleoriver hypothesis. The onset of isolation of Borneo from mainland Asia triggered the initial diversification of the group (c. 31–22 Ma). The late colonization of Java and Sumatra occurred through several independent dispersal events, poorly explained by Pleistocene sea‐level changes and frequently followed by in situ diversification.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes.

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211 genera, and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 Ma during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity. [Biodiversity; Characiformes; macroevolution; Neotropics; phylogenomics; ultraconserved elements.].

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin.

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Fossil apes and human evolution.

Humans diverged from apes (chimpanzees, specifically) toward the end of the Miocene ~9.3 million to 6.5 million years ago. Understanding the origins of the human lineage (hominins) requires reconstructing the morphology, behavior, and environment of the chimpanzee-human last common ancestor. Modern hominoids (that is, humans and apes) share multiple features (for example, an orthograde body plan facilitating upright positional behaviors). However, the fossil record indicates that living hominoids constitute narrow representatives of an ancient radiation of more widely distributed, diverse species, none of which exhibit the entire suite of locomotor adaptations present in the extant relatives. Hence, some modern ape similarities might have evolved in parallel in response to similar selection pressures. Current evidence suggests that hominins originated in Africa from Miocene ape ancestors unlike any living species.

Phylogenomic conflict coincides with rapid morphological innovation

Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between instances of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.

Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology.

Currently, Tigers (the top predator of an ecosystem) are on the list of endangered species. Thus the need is to understand the tiger's population genomics to design their conservation strategies. We analyzed the molecular evolution of tiger diversity using NADH dehydrogenase subunit 4 (ND4), a significant electron transport chain component. We have analyzed nucleotide composition and distribution pattern of ND genes, molecular evolution, evolutionary conservation pattern and conserved blocks of NADH, phylogenomics of ND4, and estimating species divergence, etc., using different bioinformatics tools and software, and MATLAB programming and computing environment. The nucleotide composition and distribution pattern of ND genes in the tiger genome demonstrated an increase in the number of adenine (A) and a lower trend of A+T content in some place of the distribution analysis. However, the observed distributions were not significant (P > 0.05). Evolutionary conservation analysis showed three highly align blocks (186 to 198, 406 to 416, and 527 to 545). On mapping the molecular evolution of ND4 among model species (n = 30), we observed its presence in a broader range of species. ND4 based molecular evolution of tiger diversity and time divergence for a tiger (20 different other species) shows that genus Panthera originated more or less at a similar time. The nucleotide composition and nucleotide distribution pattern of tiger ND genes showed the evolutionary pattern and origin of tiger and Panthera lineage concerning the molecular clock, which will help to understand their adaptive evolution.

The role of the isolation of the marginal seas during the Pleistocene in the genetic structure of black sea bream Acanthopagrus schlegelii (Bleeker, 1854) in the coastal waters of Japan.

The black sea bream Acanthopagrus schlegelii (Bleeker, 1854) is a commercially important species in Japanese waters. Assessing its population structure is essential to ensure its sustainability. In the Northwestern Pacific, historical glacial and interglacial periods during the Pleistocene have shaped the population structure of many coastal marine fishes. However, whether these events affected the population of black sea bream remains unknown. To test this hypothesis and to assess the population structure of black sea bream, we used 1,046 sequences of the mitochondrial control region from individuals collected throughout almost the entire Japanese coastal waters and combined them with 118 sequences from populations distributed in other marginal seas of the Northwestern Pacific Ocean. As in other coastal marine fish with similar distribution, we also found evidence that the glacial refugia on the marginal seas prompted the formation of three lineages in black sea bream. These lineages present signatures of population growth that coincided with the interglacial periods of the Pleistocene. While the origin of Lineages B and C remains unclear, the higher relative frequency of Lineage A in the southernmost location suggests its origin in the South China Sea. The non-significant pairwise ΦST and AMOVA of Japanese populations and the presence of these three lineages mixed in Japanese waters; strongly suggest that these lineages are homogenized in both the Sea of Japan and the Pacific Ocean. Our results indicate that the black sea bream should be managed as a single stock in Japan until the strength of connectivity in contemporary populations is further addressed using non-coding nuclear markers.

Analisis Filogenetik Cyprinus carpio Ruang Lingkup Asia Timur Dan Eropa Berdasarkan Genom Mitokondria

Carp (Cyprinus carpio L.) is one of the oldest and most commercially cultivated freshwater fish in the World. However, there are still many undetermined phylogenetic relationships and the origins of common goldfish lineages, which are an obstacle to the conservation and genetic reproduction of this species. In the process of phylogenetic analysis, researchers used mitochondrial genomes where the genomic DNA was obtained from homozygous double haploid clonal lines from domesticated Songpu strains, and the total genomic DNA was extracted and sequenced using next-generation sequencing technology. Complete mitochondrial genome sequencing of 11 individuals representing East Asia and Europe and phylogenetic analysis was performed. The purpose of this study is to provide information about the phenology of Cyprinus carpio fish, which is expected to be the basis for increasing understanding to determine the kinship relationship between Cyprinus carpio in East Asia and Europe. The results showed that the relationship between Cyprinus carpio color, Cyprinus carpio songpu mirror carp, Cyprinus carpio carpio, and Cyprinus carpio wuyuanensis was very close, this can be seen from the bootstrap value of 100%. Meanwhile, with Cyprinus carpio haematopterus has a bootstrap value of 70%. Meanwhile, with Cyprinus xingguonensis it has a bootstrap value of 66%. Furthermore, it can also be said that the Songpu mirror goldfish is closely related to C. carpio carpio which is also a member of the genus Cyprinu. The genus Cyprinu has a close relationship with the genus Catla. In the phylogenetic tree, this species of fish forms a very coherent group, supported by a high bootstrap value of 100% and an average genetic distance of 0.02. &#x0D; Key words: Mitochondrial genome, Phylogenetics, general Cyprinus carpio

Lineage tracing of Foxd1-expressing embryonic progenitors to assess the role of divergent embryonic lineages on adult dermal fibroblast function.

Recent studies have highlighted the functional diversity of dermal fibroblast populations in health and disease, with part of this diversity linked to fibroblast lineage and embryonic origin. Fibroblasts derived from foxd1‐expressing progenitors contribute to the myofibroblast populations present in lung and kidney fibrosis in mice but have not been investigated in the context of dermal wound repair. Using a Cre/Lox system to genetically track populations derived from foxd1‐expressing progenitors, lineage‐positive fibroblasts were identified as a subset of the dermal fibroblast population. During development, lineage‐positive cells were most abundant within the dorsal embryonic tissues, contributing to the developing dermal fibroblast population, and remaining in this niche into adulthood. In adult mice, assessment of fibrosis‐related gene expression in lineage‐positive and lineage‐negative populations isolated from wounded and unwounded dorsal skin was performed, identifying an enrichment of transcripts associated with matrix synthesis and remodeling in the lineage‐positive populations. Using a novel excisional wound model, ventral skin healed with a greatly reduced frequency of foxd1 lineage‐positive cells. This work supports that the embryonic origin of fibroblasts is an important predictor of fibroblast function, but also highlights that within disparate regions, fibroblasts of different lineages likely undergo convergent differentiation contributing to phenotypic similarities.

Hybridization, ecogeographical displacement and the emergence of new lineages – A genotyping‐by‐sequencing and ecological niche and species distribution modelling study of Sempervivum tectorum L. (Houseleek)

Ecogeographical displacement of homoploid hybrid lineages from their parents is well documented and considered an important mechanism to achieve reproductive isolation. In this study, we investigated the origin of the flowering plant species Sempervivum tectorum in the Massif Central (France) through homoploid hybridization between lineages of the species from the Rhine Gorge area (Germany) and the Pyrenees (France). We used genotyping-by-sequencing genetic data as evidence for the hybrid origin of the Massif Central lineage, and WorldClim climatic data and soil pH and soil temperature data collected by us for ecological niche and species distribution modelling. We could show that the Massif Central lineage shows hybrid admixture and that the niche of this lineage is significantly different from those of the parental lineages. In comparison with the parental niches, different variables of the niche of the hybrid lineage are intermediate, parental-combined or extreme. The different niche of the Massif Central populations thus can plausibly be interpreted as hybridization-derived. Our species distribution modelling for the Last Glacial Maximum and Mid-Holocene showed that the potential distribution of the hybrid lineage at the likely time of its origin in the Quaternary possibly was parapatric in relation to the largely sympatric distributions of the parental lineages. We hypothesize that reproductive isolation of the hybrid lineage from the parental lineages resulted from the segregation of distribution ranges by a differential response of the three lineages to a warming climate.

Distinct progenitor behavior underlying neocortical gliogenesis related to tumorigenesis

Radial glial progenitors (RGPs) give rise to the vast majority of neurons and glia in the neocortex. Although RGP behavior and progressive generation of neocortical neurons have been delineated, the exact process of neocortical gliogenesis remains elusive. Here, we report the precise progenitor behavior and gliogenesis program at single-cell resolution in the mouse neocortex. Fractions of dorsal RGPs transition from neurogenesis to gliogenesis progressively, producing astrocytes, oligodendrocytes, or both in well-defined propensities of ∼60%, 15%, and 25%, respectively, by fate-restricted "intermediate" precursor cells (IPCs). Although the total number of IPCs generated by individual RGPs appears stochastic, the output of individual IPCs exhibit clear patterns in number and subtype and form discrete local subclusters. Clonal loss of tumor suppressor Neurofibromatosis type 1 leads to excessive production of glia selectively, especially oligodendrocyte precursor cells. These results quantitatively delineate the cellular program of neocortical gliogenesis and suggest the cellular and lineage origin of primary brain tumor.

Fossil palm reading: using fruits to reveal the deep roots of palm diversity.

PREMISEFossils are essential for understanding evolutionary history because they provide direct evidence of past diversity and geographic distributions. However, resolving systematic relationships between fossils and extant taxa, an essential step for many macroevolutionary studies, requires extensive comparative work on morphology and anatomy. While palms (Arecaceae) have an excellent fossil record that includes numerous fossil fruits, many are difficult to identify due in part to limited comparative data on modern fruit structure.METHODSWe studied fruits of 207 palm species, representing nearly every modern genus, using X‐ray microcomputed tomography. We then developed a morphological data set to test whether the fossil record of fruits can improve our understanding of palm diversity in the deep past. To evaluate the accuracy with which this data set recovers systematic relationships, we performed phylogenetic pseudofossilization analyses. We then used the data set to investigate the phylogenetic relationships of five previously published fossil palm fruits.RESULTSPhylogenetic analyses of fossils and pseudofossilization of extant taxa show that fossils can be placed accurately to the tribe and subtribe level with this data set, but node support must be considered. The phylogenetic relationships of the fossils suggest origins of many modern lineages in the Cretaceous and early Paleogene. Three of these fossils are suitable as new node calibrations for palms.CONCLUSIONSThis work improves our knowledge of fruit structure in palms, lays a foundation for applying fossil fruits to macroevolutionary studies, and provides new insights into the evolutionary history and early diversification of Arecaceae.

Origin and distribution of ancient Thai pig lineages

AbstractWhether animal domestication in Mainland Southeast Asia (MSEA) developed locally or began with the introduction of domesticated pigs from present‐day China has been discussed at length. This study compared the mitochondrial control region (mtCR) sequences of ancient pig samples from various Thai archeological sites to ancient Chinese pigs and modern Asian pigs. Twenty‐one samples (including eight previously reported ones) from six archeological sites located in three areas of Thailand were applied to haplotype analysis along with 2005 sequences of ancient Chinese pigs and modern Asian pigs. The haplotype network showed that genetic diversity and relationship with ancient Chinese pigs suggested multiple origins of ancient Thai maternal lineages, located in present‐day China and MSEA, specifically Thailand. The distinct mtCR haplotypes found in western compared with those found in eastern and central ancient Thai pigs suggested two possible routes of the past migration. These routes corresponded to the movement of agriculturists from present‐day China to MSEA. Several shared haplotypes found between ancient Thai pigs from different archeological sites suggested people contact in the past. Most ancient Thai pigs left their descendants in the contemporary Asian population. Hence, it was proposed that most maternal ancestors of ancient Thai pigs migrated from present‐day Southern China to MSEA via two routes with some local gene flow degrees and left their descendants in Thailand. These results would pave the way for future studies focusing on the history of MSEA pig domestication.

Preferential snake detection in a simulated ecological experiment

According to Isbell's snake detection theory (SDT), the need to rapidly detect and thus avoid snakes had a major impact on the evolution of the primate visual system, and thus the origin and evolution of the primate lineage, as expansion of the visual sense is a key characteristic of primates. The SDT rests on the assumption that there are both cortical (conscious) and subcortical (unconscious) brain structures and pathways that are responsible for rapid visual detection of and quick avoidance reactions to snakes. Behavioral evidence for the SDT primarily comes from visual search tasks and presentations of images on a computer screen; our aim was to evaluate the SDT under more ecologically valid circumstances. We asked participants to take a virtual hike in which a realistic model of a snake, rabbit, or bottle had been placed on the trail. Subjects were instructed simply to imagine themselves as the hiker while watching the video. We measured heart rate and skin conductance reactions while the participants viewed the video. After the video, the participants were shown pictures of the three stimuli and asked if they had seen any of them. We found that snakes were detected more often than rabbits or bottles, and that participants showed greater changes in heart rate and greater skin conductance responses in the snake condition than in the other two conditions, even when the participant did not report having seen the snake. A critical component of the SDT is that primates must be able to quickly detect snakes even when their attention is directed elsewhere. Using a novel experimental context-a simulated hike-we assessed arousal and detection without directing participants to attend to any particular stimulus or event. Our data support the SDT by providing evidence of enhanced detection and autonomic arousal even in the absence of detection. Replication of these results using additional controls and experimental contexts will help refine our understanding of snake avoidance by primates.

The evolutionary history of sedges (Cyperaceae) in Madagascar

AbstractAimMadagascar is renowned for its unparalleled biodiversity and endemism. With many ecosystems under threat, research is urgently needed on its unique plant diversity. This applies both to Madagascar's forests and treeless vegetation types. Sedges (Cyperaceae) are among the top 10 species‐richest angiosperm families in Madagascar (310 native species, 38% endemic), of which two‐thirds occur in open habitats. We aimed to infer the evolutionary history of sedges in Madagascar, by estimating the number, age and origins of endemic lineages, and how they diversified on the island. We tested contrasting hypotheses of (a) few colonizations but important in situ radiations against (b) a high number of anagenetic colonizations.LocationMadagascar and the surrounding Indian Ocean islands, integrated within a global dataset.TaxonSedge family Cyperaceae.MethodsWe estimated time‐calibrated molecular phylogenies encompassing a large proportion of Madagascar's known sedge flora (incl. 55% of native species), integrating sequence data for 1,382 accessions representing almost 25% of the c. 5,600 sedge species worldwide, combined with ancestral area reconstruction, diversification analyses and Bayesian stochastic mapping.ResultsCyperaceae lineages arrived in Madagascar from c. 40 Mya with many arriving more recently. About 20 endemic lineages of Cyperaceae occur on the island, of which only six encompass more than five species. All except one of the endemic lineages that diversified in Madagascar use the C3 photosynthetic pathway. The main biogeographical links of Madagascar's sedge flora are to Southern and Tropical Africa.Main conclusionsThe biogeographical history of Cyperaceae in Madagascar is a chronicle of relatively recent multiple in and out processes of long‐distance dispersal colonizations constrained by distance. Also, the Madagascar region is not only a ‘sink’ for immigrant taxa, in situ diversification and dispersal to other regions also occurred. Some of the most diverse endemic lineages show clear adaptation to local environments.

On the Origins of the Genetic Lineage of the Rurikids as an Issue not Related to the “Normanist Problem” [Proiskhozhdenie geneticheskoi linii Riurikovichei: nezavisimost’ ot “normanskoi problemy”

On the Origins of the Genetic Lineage of the Rurikids as an Issue not Related to the “Normanist Problem” [Proiskhozhdenie geneticheskoi linii Riurikovichei: nezavisimost’ ot “normanskoi problemy”

Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs

Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply sufficient time for species-level divergence. To understand why this species appears unified while congeners have radiated, we analyze and compare male advertisement calls, mitochondrial, and nuclear markers and speak to the complex processes that have potentially influenced its contemporary patterns. We find extensive geographic and topological mitonuclear discordance, with three nuclear lineages containing 6 more-structured mtDNA lineages, and nuclear introgression at some contact zones. Male advertisement call differentiation is incongruent with the genetic structure as only one lineage appears differentiated. Occupying the Interior Highlands of the central United States, this Western lineage also has the most concordant mitochondrial and nuclear geographic patterns. Based on our findings we suggest that the antiquity of common ancestors was not as important as the maintenance of allopatry in the divergence in P. crucifer genetic lineages. We use multiple lines of evidence to generate hypotheses of isolation, reticulation, and discordance within this species and to expand our understanding of the early stages of speciation.

Evolution and epidemiologic dynamics of dengue virus in Nicaragua during the emergence of chikungunya and Zika viruses.

Arthropod-borne viruses (arboviruses) comprise a significant and ongoing threat to human health, infecting hundreds of millions annually. Three such arboviruses include circumtropical dengue, Zika, and chikungunya viruses, exhibiting continuous emergence primarily via Aedes mosquito vectors. Nicaragua has experienced endemic dengue virus (DENV) transmission involving multiple serotypes since 1985, with chikungunya virus (CHIKV) reported in 2014-2015, followed by Zika virus (ZIKV) first reported in 2016. In order to identify patterns of genetic variation and selection pressures shaping the evolution of co-circulating DENV serotypes in light of the arrival of CHIKV and ZIKV, we employed whole-genome sequencing on an Illumina MiSeq platform of random-amplified total RNA libraries to characterize 42 DENV low-passage isolates, derived from viremic patients in Nicaragua between 2013 and 2016. Our approach also revealed clinically undetected co-infections with CHIKV. Of the three DENV serotypes (1, 2, and 3) co-circulating during our study, we uncovered distinct patterns of evolution using comparative phylogenetic inference. DENV-1 genetic variation was structured into two distinct co-circulating lineages with no evidence of positive selection in the origins of either lineage, suggesting they are equally fit. In contrast, the evolutionary history of DENV-2 was marked by positive selection, and a unique, divergent lineage correlated with high epidemic potential emerged in 2015 to drive an outbreak in 2016. DENV-3 genetic variation remained unstructured into lineages throughout the period of study. Thus, this study reveals insights into evolutionary and epidemiologic trends exhibited during the circulation of multiple arboviruses in Nicaragua.

Comparative genomics of Fusarium oxysporum f. sp. melonis strains reveals nine lineages and a new sequence type of AvrFom2.

Summary Fusarium oxysporum f. sp. melonis (Fom) is one of the most important pathogens of melon worldwide. In this study, we investigated the genomic diversity of Fom. One of the aims was to find clues for the origin(s) and dispersal of clonal lineages and races of Fom. We therefore included a large number of Fom strains from Iran, where melon has been cultivated for at least 5000 years. In 33 new genome sequences of Fom strains from different geographical regions of Iran and across the world, 40 new candidate effector genes were identified. Presence/absence of candidate effector genes and phylogenetic analyses resolved nine Fom lineages. The presence of a highly similar set of effector genes in some distant lineages is suggestive of horizontal chromosome transfer, a process known to occur in the Fusarium oxysporum species complex. Race 1.2, which breaks both Fom1 and Fom2 resistance genes, occurs in three of the nine lineages, two of which are predominant in Iran. We also identified a new sequence type of the AVRFom2 avirulence gene in one lineage. Expression of this sequence type during melon infection and genetic complementation suggest that this sequence type is not recognized by the Fom2 resistance protein.

The Legacy of Recurrent Introgression during the Radiation of Hares.

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1–4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation. [Adaptation; ancient introgression; hybridization; Lepus; phylogenomics.]