Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

BACKGROUND: In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. METHODS: Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. RESULTS: Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. CONCLUSIONS: The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species

Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus

Idiopathic congenital nystagmus (ICN) is characterised by involuntary, periodic, predominantly horizontal, oscillations of both eyes. We identified 22 mutations in FRMD7 in 26 families with X-linked idiopathic congenital nystagmus. Screening of 42 ICN singleton cases (28 male, 14 females) yielded three mutations (7%). We found restricted expression of FRMD7 in human embryonic brain and developing neural retina suggesting a specific role in the control of eye movement and gaze stability

Crataegus subg. Sanguineae_collection sites + ecological variables

Localities and climate, soil, and habitat variables which were collected from 2010-2013. Dist.to."X" refers to the distance from the site to the nearest agriculture, road, or aboveground water source, %"X" refers to the percent coverage of different substrates, and soil."X" refers to soil characteristics

Crataegus subg. Sanguineae_microsatellite data_binary form for genodive

Microsatellite data, coded as binary (Present=7, Absent=9) in the format for GenoDive for all species and cytotypes sampled from Crataegus subg. Sanguineae. Column headers for the genetic data are coded with the name of the locus followed by a period followed by the allele size variant

Crataegus subg Americanae + Sanguineae_localities and bioclim data

This excel sheet represents the localities from which distributions and ecological climate niches were created for Pacific Northwest members of Crataegus subg. Sanguineae, and subg. Americanae. Alt= altitude, bio1-19 refer to Bioclim variables 1-19, available here: http://www.worldclim.org/biocli

Niche Shifts, Hybridization, Polyploidy and Geographic Parthenogenesis in Western North American Hawthorns (Crataegus subg. Sanguineae, Rosaceae)

We compare biogeographic and morphological parameters of two agamic complexes of western North American hawthorns so as to evaluate possible explanations of the differences in range between sexually reproducing taxa and their apomictic sister taxa. We have documented range, breeding system, morphology, leaf vascular architecture, and niche breadth in these hawthorns, for which phylogenetic relationships and ploidy levels are known. Species distribution data from herbarium specimens and online databases were analyzed in order to compare ranges and climate niches described by bioclimatic variables. Flow cytometry documented ploidy level and breeding system. Voucher specimens provided morphometric data that were analyzed using uni- and multivariate methods. Members of two black-fruited taxonomic sections of Crataegus subg. Sanguineae (sections Douglasianae, Salignae) have previously been identified as hybrids. They are presumptively self-fertile polyploids with pseudogamous gametophytic apomixis. Their morphologies, geographic ranges, and niche characteristics resemble those of their diploid, sexual parent or are intermediate between them and those of their other parent, one or both of two partially sympatric tetraploid apomicts in red-fruited C. subg. Americanae with much wider distributions. Comparing sections Douglasianae and Salignae suggests that geographic parthenogenesis (larger range sizes in apomicts, compared to sexually reproducing taxa) may have less to do with adaptation than it does with reproductive assurance in the pseudogamously apomictic and self-compatible hybrids. Greater climate niche breadth in allopolyploids compared to diploids similarly may be more due to parental traits than to effects of genome duplication per se

Niche Shifts, Hybridization, Polyploidy and Geographic Parthenogenesis in Western North American Hawthorns (Crataegus subg. Sanguineae, Rosaceae)

We compare biogeographic and morphological parameters of two agamic complexes of western North American hawthorns so as to evaluate possible explanations of the differences in range between sexually reproducing taxa and their apomictic sister taxa. We have documented range, breeding system, morphology, leaf vascular architecture, and niche breadth in these hawthorns, for which phylogenetic relationships and ploidy levels are known. Species distribution data from herbarium specimens and online databases were analyzed in order to compare ranges and climate niches described by bioclimatic variables. Flow cytometry documented ploidy level and breeding system. Voucher specimens provided morphometric data that were analyzed using uni- and multivariate methods. Members of two black-fruited taxonomic sections of Crataegus subg. Sanguineae (sections Douglasianae, Salignae) have previously been identified as hybrids. They are presumptively self-fertile polyploids with pseudogamous gametophytic apomixis. Their morphologies, geographic ranges, and niche characteristics resemble those of their diploid, sexual parent or are intermediate between them and those of their other parent, one or both of two partially sympatric tetraploid apomicts in red-fruited C. subg. Americanae with much wider distributions. Comparing sections Douglasianae and Salignae suggests that geographic parthenogenesis (larger range sizes in apomicts, compared to sexually reproducing taxa) may have less to do with adaptation than it does with reproductive assurance in the pseudogamously apomictic and self-compatible hybrids. Greater climate niche breadth in allopolyploids compared to diploids similarly may be more due to parental traits than to effects of genome duplication per se

Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria

Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia), a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community, either directly though changes in the soil chemistry or indirectly through altered host legume feedbacks, and is potentially a strong selective agent acting on natural rhizobia populations

Species richness, distribution and genetic diversity of <it>Caenorhabditis</it> nematodes in a remote tropical rainforest

Abstract Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species.</p

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

Abstract Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species