The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology.

BACKGROUND: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. FINDINGS: We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog. CONCLUSIONS: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology.

Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings: We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog. Conclusions: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

The Australian dingo is an early offshoot of modern breed dogs.

Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.

Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean.

Two new species of miniature silverside fishes are described from coastal habitats in the tropical Atlantic: Membras pygmaea sp. nov., from Brus Lagoon, Honduras, and M. procera sp. nov., from the Gulf of Urabá, Colombia. These new species belong to the martinica species-group within the genus Membras Bonaparte. The monophyletic martinica species-group (see below) contains four additional species, all coastal, marine that extend from the east coast of North America to São Paolo State, Brazil. Within the martinica species-group, all but M. martinica are miniature species, ranging from 41-60 mm SL. The smallest species, M. pygmaea sp. nov., is mature at 24 mm SL. A geometric morphometric analysis shows: (i) each species of the martinica species-group occupies its own portion of shape space; and (ii) none of the miniature species possess the shapes of small immature M. martinica. While some of the literature suggests that miniaturization may involve paedomorphosis, our results show that the miniatures accelerate to adult body forms.

Estimation of short-term C-fixation in a New England temperate tidal freshwater wetland.

Wetlands provide myriad ecosystem services, yet the C-cycling of vegetation within interior freshwater tidal wetlands remains poorly understood. To this end, we estimated species'-specific plant carbon-fixation rates for the six dominant wetland plant species in a large temperate freshwater wetland in Connecticut, USA. We integrated field C-fixation rates for dominant marsh plant species with satellite-derived leaf area index and wetland aerial extent data to: 1) quantify seasonal and species-level differences in wetland plant C-fixation rates; and 2) estimate whole-marsh emergent aquatic plant C-fixation rates over the growing season. Photosynthetic rates differed significantly by species and month (P < 0.05). Acorus calamus had the highest photosynthetic rate between May and September, and Acer saccharinum had the lowest. By integrating field photosynthetic data with wetland aerial extents, we estimated that the total annual C uptake by the vegetation in this wetland, which was 2868 Mg C. Herbaceous vegetation contributed to most of that stock (herbaceous vegetation = 2099.2 Mg C, forest = 769.6 Mg C), although soil respiration likely offset those numbers substantially. Our results demonstrate the importance of short-term above-ground freshwater wetland C-fixation, and that the emergent vegetative component of these wetland systems are key components of the tidal freshwater wetland C cycle.

Insight into the population structure of hardhead silverside, Atherinomorus stipes (Teleostei: Atherinidae), in Belize and the Florida Keys using nd2.

Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island-based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island-groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well-supported monophyletic groups: a Belizean-type clade and a Floridian-type clade, indicating potential species-level differentiation.

Effects of Dam Removal on Fish Community Interactions and Stability in the Eightmile River System, Connecticut, USA.

New multivariate time-series methods have the potential to provide important insights into the effects of ecosystem restoration activities. To this end, we examined the temporal effects of dam removal on fish community interactions using multivariate autoregressive models to understand changes in fish community structure in the Eightmile River System, Connecticut, USA. We sampled fish for 6 years during the growing season; 1 year prior to, 2 years during, and for 3 years after a small dam removal event. The multivariate autoregressive analysis revealed that the site above the dam was the most reactive and least resilient sample site, followed in order by the below-dam and nearby reference site. Even 3 years after the dam removal event, the stream was still in a recovery stage that had failed to approximate the community structure of the reference site. This suggests that the reorganization of fish communities following dam removals, with the goal of ecological restoration, may take decades to centuries for the restored sites to approximate the community structure of nearby undisturbed sites. Results from this study also highlight the utility of multivariate autoregressive modeling for examining temporal interactions among species in response to adaptive management activities both in aquatic systems and elsewhere.

Fish assemblage response to a small dam removal in the Eightmile River system, Connecticut, USA.

We examined the effects of the Zemko Dam removal on the Eightmile River system in Salem, Connecticut, USA. The objective of this research was to quantify spatiotemporal variation in fish community composition in response to small dam removal. We sampled fish abundance over a 6-year period (2005-2010) to quantify changes in fish assemblages prior to dam removal, during drawdown, and for three years following dam removal. Fish population dynamics were examined above the dam, below the dam, and at two reference sites by indicator species analysis, mixed models, non-metric multidimensional scaling, and analysis of similarity. We observed significant shifts in fish relative abundance over time in response to dam removal. Changes in fish species composition were variable, and they occurred within 1 year of drawdown. A complete shift from lentic to lotic fishes failed to occur within 3 years after the dam was removed. However, we did observe increases in fluvial and transition (i.e., pool head, pool tail, or run) specialist fishes both upstream and downstream from the former dam site. Our results demonstrate the importance of dam removal for restoring river connectivity for fish movement. While the long-term effects of dam removal remain uncertain, we conclude that dam removals can have positive benefits on fish assemblages by enhancing river connectivity and fluvial habitat availability.

Diversity in neotropical wet forests during the Cenozoic is linked more to atmospheric CO2 than temperature.

Models generally predict a response in species richness to climate, but strong climate-diversity associations are seldom observed in long-term (more than 10(6) years) fossil records. Moreover, fossil studies rarely distinguish between the effects of atmospheric CO2 and temperature, which limits their ability to identify the causal controls on biodiversity. Plants are excellent organisms for testing climate-diversity hypotheses owing to their strong sensitivity to CO2, temperature and moisture. We find that pollen morphospecies richness in an angiosperm-dominated record from the Palaeogene and early Neogene (65-20 Ma) of Colombia and Venezuela correlates positively to CO2 much more strongly than to temperature (both tropical sea surface temperatures and estimates of global mean surface temperature). The weaker sensitivity to temperature may be due to reduced variance in long-term climate relative to in higher latitudes, or to the occurrence of lethal or sub-lethal temperatures during the warmest times of the Eocene. Physiological models predict that productivity should be the most sensitive to CO2 within the angiosperms, a prediction supported by our analyses if productivity is linked to species richness; however, evaluations of non-angiosperm assemblages are needed to more completely test this idea.

Postglacial recolonization of eastern Blacknose Dace,Rhinichthys atratulus(Teleostei: Cyprinidae), through the gateway of New England.

During the last ice age, much of North America far south as 40°N was covered by glaciers (Hewitt 2000). About 20,000 years ago, as the glaciers retreated, the hydrologic landscape changed dramatically creating waterways for fish dispersal. The number of populations responsible for recolonization and the regions from which they recolonized are unknown for many freshwater fishes living in New England and southeastern Canada. The Blacknose Dace,Rhinichthys atratulus, is one of the freshwater fish species that recolonized this region. We hypothesize that the earliest deglaciated region, modern-day Connecticut, was recolonized byR. atratulusvia a single founding event by a single population. In this paper, we test this hypothesis phylogenetically with regard to the major drainage basins within Connecticut. The mitochondrial DNA exhibits low nucleotide diversity, high haplotype diversity, and a dominant haplotype found across the state. A small percentage of individuals in the Housatonic drainage basin, however, share a haplotype with populations in New York drainage basins, a haplotype not found elsewhere in Connecticut's drainage basins. We calculated a range for the rate of divergence for NADH dehydrogenase subunit 2 (nd2) and control region (ctr) of 4.43-6.76% and 3.84-8.48% per million years (my), respectively. While this range is higher than the commonly accepted rate of 2% for mitochondrial DNA, these results join a growing list of publications finding high rates of divergence for various taxa (Peterson and Masel 2009). The data support the conclusion that Connecticut as a whole was recolonized initially by a single founding event that came from a single refugium. Subsequently, the Housatonic basin alone experienced a secondary recolonization event.

Distributional congruence among aquatic plants: invertebrates and fishes withim the Río Paraguay Basin, Paraguay

Hipótesis nulas concernientes a distribuciones de especies al azar con respecto a subregiones y macrohábitats dentro del Río Paraguay son examinadas con datos provenientes de 131 especies de macrocrustáceos e invertebrados bénticos y 186 especies de plantas acuáticas. Los patrones son comparados con el resultado de distrubuciones de peces presentedos por Chernoff et al. (2004). Los datos provenientes de invertebrados mostraron un patrón identico entre subregiones, como es evidente en las distribuciones de peces. Los resulatdos apoyan el reconocimiento de dos zonas:i) la zona del Río Paraguay incluyendo las regiones superiores e inferiores del Río Negro, ii) la zona del Río Apa incluyendo el Río Apa y el Riacho La Paz. Para todos los grupos de datos, la zona del Río Paraguay posee una mayor riqueza de especies que la zona del Río Apa. La frontera entre las zonas es abrupta, lo cual es tamién apoyado por los datos provenientes de las plantas. Solo 11 de 186 especies de plantas fueron encontradas en ambas zonas. No existen patrones de congruencia entre macrohábotats. Datos de plantas e invertebrados contienen muchos valores que no son diferentes de las medias de similaridades al azar. Los datos provenientes de las plantas demuestra una relación entre hábitats de orilla y arena, los cuales están más sometidos a grandes corrientes que los otros hábitats. Las plantas encontradas en hábitats de aguas negras poseen poca similaridad con otros macrohábitats. Basado en estas observaciones, se concluye que habitats significantes dentro de cada zona deben ser preservados para mantener una gran porción de la biodiversidad

Divergence of mitochondrial dna is not corroborated by nuclear dna, morphology, or behavior in Drosophila simulans.

We ask whether the observed mitochondrial DNA (mtDNA) population subdivision of Drosophila simulans is indicative of organismal structure or of specific processes acting on the mitochondrial genome. Factors either intrinsic or extrinsic to the host genome may influence the evolutionary dynamics of mtDNA. Potential intrinsic factors include adaptation of the mitochondrial genome and of nucleomitochondrial gene complexes specific to the local environment. An extrinsic force that has been shown to influence mtDNA evolution in invertebrates is the bacterial endosymbiont Wolbachia. Evidence presented in this study suggests that mtDNA is not a good indicator of organismal subdivision in D. simulans. Furthermore, there is no evidence to suggest that Wolbachia causes any reduction in nuclear gene flow in this species. The observed differentiation in mtDNA is not corroborated by data from NADH: ubiquinone reductase 75kD subunit precursor or the Alcohol dehydrogenase-related loci, from the shape or size of the male genital arch, or from assortative premating behavior. We discuss these results in relation to a mitochondrial genetic species concept and the potential for Wolbachia-induced incompatibility to be a mechanism of speciation in insects. We conclude with an iterated appeal to include phylogenetic and statistical tests of neutrality as a supplement to phylogenetic and population genetic analyses when using mtDNA as an evolutionary marker.

Bryconops humeralis y B.vibex, dos nuevas especies del genero bryconops kner (1858) para Venezuela / Bryconops humeralis and B.vibex two new species of the genus bryconops kner (1858) for Venezuela

Este trabajo presenta la descripción de dos nuevas especies género Bryconops Kner (1858) para Venezuela: Bryconops humeralis y Bryconops vibex. Estas especies son comunes en los ríos de la cuenca del orinoco en el Estado Amazonas (Venezuela). Ambas especies poseen manchas humeral sencilla, sin embargo ellas se diferencian por los siguientes caracteres: En B.vibex el cuerpo robusto, hocico, maxilar y aletas pélvicas alargados; B.humeralis posee un número menor de series de escamas bajo la línea lateral 4-5 vs 6 en B.vibex. Junto con Bryconops inpai, son las únicas especies del género que poseen mancha humeral. Sin embargo, en esta última especie la mancha es doble en lugar de sencilla