It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times ...domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In ...addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.
Objective
To explore possible changes in the community attributes of haematophagous insects as a function of forest disturbance. We compare the patterns of diversity and abundance, plus the ...behavioural responses of three epidemiologically distinct vector assemblages across sites depicting various levels of forest cover.
Methods
Over a 3‐year period, we sampled mosquitoes, sandflies and biting‐midges in forested habitats of central Panama. We placed CDC light traps in the forest canopy and in the understorey to gather blood‐seeking females.
Results
We collected 168 405 adult haematophagous dipterans in total, including 26 genera and 86 species. Pristine forest settings were always more taxonomically diverse than the disturbed forest sites, confirming that disturbance has a negative impact on species richness. Species of Phlebotominae and Culicoides were mainly classified as climax (i.e. forest specialist) or disturbance‐generalist, which tend to decrease in abundance along with rising levels of disturbance. In contrast, a significant portion of mosquito species, including primary and secondary disease vectors, was classified as colonists (i.e. disturbed‐areas specialists), which tend to increase in numbers towards more disturbed forest habitats. At pristine forest, the most prevalent species of Phlebotominae and Culicoides partitioned the vertical niche by being active at the forest canopy or in the understorey; yet this pattern was less clear in disturbed habitats. Most mosquito species were not vertically stratified in their habitat preference.
Conclusion
We posit that entomological risk and related pathogen exposure to humans is higher in pristine forest scenarios for Culicoides and Phlebotominae transmitted diseases, whereas forest disturbance poses a higher entomological risk for mosquito‐borne infections. This suggests that the Dilution Effect Hypothesis (DEH) does not apply in tropical rainforests where highly abundant, yet unrecognised insect vectors and neglected zoonotic diseases occur. Comprehensive, community level entomological surveillance is, therefore, the key for predicting potential disease spill over in scenarios of pristine forest intermixed with anthropogenic habitats. We suggest that changes in forest quality should also be considered when assessing arthropod‐borne disease transmission risk.
Objectif
Explorer les changements possibles dans les attributs communautaires des insectes hématophages en fonction de la perturbation des forêts. Nous comparons les modèles de diversité et d'abondance, ainsi que les réponses comportementales de trois assemblages de vecteurs épidémiologiquement distincts sur des sites illustrant divers niveaux de couverture forestière.
Méthodes
Au cours d'une période de trois ans, nous avons échantillonné des moustiques, des phlébotomes et des moucherons piqueurs dans les habitats forestiers du centre de Panama. Nous avons placé des pièges à lumière CDC dans la canopée de la forêt et dans le sous‐étage pour recueillir les femelles en quête de sang.
Résultats
Nous avons collecté un total de 168.405 diptères hématophages adultes, dont 26 genres et 86 espèces. Les environnements de forêt intacts étaient toujours plus diversifiés du point de vue taxonomique que les sites forestiers perturbés, confirmant que les perturbations avaient un impact négatif sur la richesse en espèces. Les espèces de phlébotome et Culicoïdes étaient principalement classés comme climax (spécialiste de la forêt) ou généralistes de perturbation, qui ont tendance à diminuer en abondance parallèlement aux niveaux croissants de perturbation. En revanche, une partie importante des espèces de moustiques, y compris les vecteurs primaires et secondaires de maladies, a été classée dans la catégorie des colons (c'est‐à‐dire spécialistes des zones perturbées), qui ont tendance à se multiplier vers des habitats forestiers plus perturbés. Dans la forêt vierge, les espèces de phlébotomes et Culicoïdes les plus répandues cloisonnaient la niche verticale en étant actives dans la canopée de la forêt ou dans le sous‐étage; pourtant, cette tendance était moins nette dans les habitats perturbés. La plupart des espèces de moustiques n’étaient pas stratifiées verticalement dans leur préférence d'habitat.
Conclusion
Nous estimons que le risque entomologique et l'exposition associée des agents pathogènes à l'homme est plus élevé dans les scénarios de forêt vierge pour les maladies transmises par les phlébotomes et Culicoïdes, alors que la perturbation des forêts pose un risque entomologique plus élevé pour les infections transmises par les moustiques. Cela suggère que l'hypothèse de l'effet de dilution ne s'applique pas dans les forêts tropicales humides où se reproduisent très abondamment les insectes vecteurs, mais non reconnus, et où des maladies zoonotiques négligées surviennent. Une surveillance entomologique approfondie au niveau de la communauté est donc la clé pour prédire le potentiel de propagation des maladies dans des scénarios de forêt vierge mélangée à des habitats anthropiques. Nous suggérons que les changements dans la qualité des forêts soient également pris en compte lors de l’évaluation du risque de propagation de maladies transmises par les arthropodes.
The Intermediate Disturbance Hypothesis (IDH) is well-known in ecology providing an explanation for the role of disturbance in the coexistence of climax and colonist species. Here, we used the IDH as ...a framework to describe the role of forest disturbance in shaping the mosquito community structure, and to identify the ecological processes that increase the emergence of vector-borne disease. Mosquitoes were collected in central Panama at immature stages along linear transects in colonising, mixed and climax forest habitats, representing different levels of disturbance. Species were identified taxonomically and classified into functional categories (i.e., colonist, climax, disturbance-generalist, and rare). Using the Huisman-Olff-Fresco multi-model selection approach, IDH testing was done. We did not detect a unimodal relationship between species diversity and forest disturbance expected under the IDH; instead diversity peaked in old-growth forests. Habitat complexity and constraints are two mechanisms proposed to explain this alternative postulate. Moreover, colonist mosquito species were more likely to be involved in or capable of pathogen transmission than climax species. Vector species occurrence decreased notably in undisturbed forest settings. Old-growth forest conservation in tropical rainforests is therefore a highly-recommended solution for preventing new outbreaks of arboviral and parasitic diseases in anthropic environments.
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► Taxonomic groupings within the frog genus Pristimantis are unsupported by our 5-gene phylogenetic analysis. ► Within the genus Pristimantis we estimate at least 11 independent ...colonization events from South to Central America. ► At least eight invasions took place before 3.5million years ago, the assumed date for the completion of the Isthmus. ► Land connections between Central and South America may have formed earlier than is often assumed. ► The old age of lineages endemic to Panama suggests the presence of cryptic taxa.
The completion of the land bridge between North and South America approximately 3.5–3.1million years ago (Ma) initiated a tremendous biogeographic event called the Great American Biotic Interchange (GABI), described principally from the mammalian fossil record. The history of biotic interchange between continents for taxonomic groups with poor fossil records, however, is not well understood. Molecular and fossil data suggest that a number of plant and animal lineages crossed the Isthmus of Panama well before 3.5Ma, leading biologists to speculate about trans-oceanic dispersal mechanisms. Here we present a molecular phylogenetic analysis of the frog genus Pristimantis based on 189 individuals of 137 species, including 71 individuals of 31 species from Panama and Colombia. DNA sequence data were obtained from three mitochondrial (COI, 12S, 16S) and two nuclear (RAG-1 and Tyr) genes, for a total of 4074 base pairs. The resulting phylogenetic hypothesis showed statistically significant conflict with most recognized taxonomic groups within Pristimantis, supporting only the rubicundus Species Series, and the Pristimantis myersi and Pristimantis pardalis Species Groups as monophyletic. Inference of ancestral areas based on a likelihood model of geographic range evolution via dispersal, local extinction, and cladogenesis (DEC) suggested that the colonization of Central America by South American Pristimantis involved at least 11 independent events. Relaxed-clock analyses of divergence times suggested that at least eight of these invasions into Central America took place prior to 4Ma, mainly in the Miocene. These findings contribute to a growing list of molecular-based biogeographic studies presenting apparent temporal conflicts with the traditional GABI model.
The Global Genome Biodiversity Network (GGBN) was formed in 2011 with the principal aim of making high-quality well-documented and vouchered collections that store DNA or tissue samples of ...biodiversity, discoverable for research through a networked community of biodiversity repositories. This is achieved through the GGBN Data Portal (http://data.ggbn.org), which links globally distributed databases and bridges the gap between biodiversity repositories, sequence databases and research results. Advances in DNA extraction techniques combined with next-generation sequencing technologies provide new tools for genome sequencing. Many ambitious genome sequencing projects with the potential to revolutionize biodiversity research consider access to adequate samples to be a major bottleneck in their workflow. This is linked not only to accelerating biodiversity loss and demands to improve conservation efforts but also to a lack of standardized methods for providing access to genomic samples. Biodiversity biobank-holding institutions urgently need to set a standard of collaboration towards excellence in collections stewardship, information access and sharing and responsible and ethical use of such collections. GGBN meets these needs by enabling and supporting accessibility and the efficient coordinated expansion of biodiversity biobanks worldwide.
Anopheles punctimacula s.l., a regional malaria vector in parts of Central America, comprises two geographically isolated lineages across Panama and Costa Rica.
•Anopheles punctimacula s.l. comprises ...two geographically isolated lineages.•Phylogenetic inference with sequences of the mitochondrial 3′ COI and the rDNA ITS2 depicted 6 well-supported lineages.•We report An. malefactor for the first time in Costa Rica, but An. calderoni was not found in Panama.
Anopheles punctimacula s.l. is a regional malaria vector in parts of Central America, but its role in transmission is controversial due to its unresolved taxonomic status. Two cryptic species, An. malefactor and An. calderoni, have been previously confused with this taxon, and evidence for further genetic differentiation has been proposed. In the present study we collected and morphologically identified adult female mosquitoes of An. punctimacula s.l. from 10 localities across Panama and one in Costa Rica. DNA sequences from three molecular regions, the three prime end of the mitochondrial cytochrome c oxidase I gene (3′ COI), the Barcode region in the five prime end of the COI (5′ COI), and the rDNA second internal transcribed spacer (ITS2) were used to test the hypothesis of new molecular lineages within An. punctimacula s.l. Phylogenetic analyses using the 3′ COI depicted six highly supported molecular lineages (A–F), none of which was An. malefactor. In contrast, phylogenetic inference with the 5′ COI demonstrated paraphyly. Tree topologies based on the combined COI regions and ITS2 sequence data supported the same six lineages as the 3′ COI alone. As a whole this evidence suggests that An. punctimacula s.l. comprises two geographically isolated lineages, but it is not clear whether these are true species. The phylogenetic structure of the An. punctimacula cluster as well as that of other unknown lineages (C type I vs C type II; D vs E) appears to be driven by geographic partition, because members of these assemblages did not overlap spatially. We report An. malefactor for the first time in Costa Rica, but our data do not support the presence of An. calderoni in Panama.
We have investigated the phylogenetic relationships among six wild and six domesticated taxa of Cucurbita using as a marker an intron region from the mitochondrial nad1 gene. Our study represents one ...of the first successful uses of a mtDNA gene in resolving inter- and intraspecific taxonomic relationships in Angiosperms and yields several important insights into the origins of domesticated Cucurbita. First, our data suggest at least six independent domestication events from distinct wild ancestors. Second, Cucurbita argyrosperma likely was domesticated from a wild Mexican gourd, Cucurbita sororia, probably in the same region of southwest Mexico that gave rise to maize. Third, the wild ancestor of Cucurbita moschata is still unknown, but mtDNA data combined with other sources of information suggest that it will probably be found in lowland northern South America. Fourth, Cucurbita andreana is supported as the wild progenitor of Cucurbita maxima, but humid lowland regions of Bolivia in addition to warmer temperate zones in South America from where C. andreana was originally described should possibly be considered as an area of origin for C. maxima. Fifth, our data support other molecular results that indicate two separate domestications in the Cucurbita pepo complex. The potential zone of domestication for one of the domesticated subspecies, C. pepo subsp. ovifera, includes eastern North America and should be extended to north eastern Mexico. The wild ancestor of the other domesticated subspecies, C. pepo subsp. pepo, is undiscovered but is closely related to C. pepo subsp. fraterna and possibly will be found in southern Mexico.
Landscape changes occurring in Panama, a country whose geographic location and climate have historically supported arbovirus transmission, prompted the hypothesis that arbovirus prevalence increases ...with degradation of tropical forest habitats. Investigations at four variably degraded sites revealed a diverse array of potential mosquito vectors, several of which are known vectors of arbovirus pathogens. Overall, 675 pools consisting of 25,787 mosquitoes and representing 29 species from nine genera (collected at ground and canopy height across all habitats) were screened for cytopathic viruses on Vero cells. We detected four isolates of Gamboa virus (family:Bunyaviridae; genus:Orthobunyavirus) from pools of Aedeomyia squamipennis captured at canopy level in November 2012. Phylogenetic characterization of complete genome sequences shows the new isolates to be closely related to each other with strong evidence of reassortment among the M segment of Panamanian Gamboa isolates and several other viruses of this group. At the site yielding viruses, Soberanía National Park in central Panama, 18 mosquito species were identified, and the predominant taxa included A. squamipennis,Coquillettidia nigricans, and Mansonia titillans.
We conducted nocturnal surveys in the insular and coastal areas of Coiba National Park (CNP) and its mainland buffer zone in Panama (Chiriquí conservation site) from 2009–2012 to determine the ...conservation status of Crocodylus acutus. In 99 nights, we surveyed 147.2 km and captured 185 animals during nocturnal transects inspection with headlamps. Overall, sex ratio was 1.00:1.01 female/male with significant differences by size/age class and year. Females were slightly larger in total length than males (115.1 ± 56.9 cm-females, 105.4 ± 71.8 cm-males). The encounter rate was calculated based on number of animals captured per km of surveyed transect. The C. acutus encounter rate per year was 1.8 ind/km (60 ind/33.5 km/12 places visited) in 2009, 1.0 ind/km (90 ind/87.4 km/18 places visited) in 2010, and 1.3 ind/km (35 ind/26.3 km/8 places visited) in 2012. Based on our spatial analysis, the animals showed a dispersed pattern in most sites on CNP. Captured C. acutus were found in 581.1 km2 total area within 78% natural habitat, including mangroves and beaches, and 22% disturbed habitat on both the mainland and the islands. In addition, the spatial analysis showed reduction in natural land cover; crocodile habitat showed limited conversion to agricultural land use; and we found correlation between crocodile population size and protected areas. The differences between mainland and island populations regarding ecology suggest that a long-term monitoring program for American Crocodiles is necessary to distinguish between natural fluctuations and anthropogenic changes on population dynamics and conservation status. Entre 2009 al 2012 hicimos varias expediciones en la parte insular y en las áreas costeras del Parque Nacional Coiba y su zona de influencia en Panamá (Sitio de conservación para la diversidad), para determinar el estado de conservación de Crocodylus acutus y sus hábitats asociados. En 99 noches recorrimos 147.2 km y capturamos 185 animales usando linternas de cabeza. La proporción de sexos fue 1.00:1.01 hembra/macho, la cual fue significativamente diferente cuando los animales fueron clasificados por grupo etario y año. Las hembras fueron un poco más grandes que los machos (115.1 ± 56.9 cm-hembras, 105.4 ± 71.8 cm-machos). La tasa de encuentro fue calculada con base en el número de animales capturados por kilómetro. La tasa de encuentro para C. acutus por año fue de 1.8 ind/km (n = 60; 33.5 km; lugares visitados: 12) en 2009, 1.0 ind/km (n = 90; 87.4 km; lugares visitados: 18) in 2010 y 1.3 ind/km (n = 35; 26.3 km; 26.3; lugares visitados: 8) en 2012. El análisis espacial mostró a C. acutus distribuido en la isla de Coiba en un patrón disperso, excepto en El María y el Playa Blanca donde el patrón de dispersión fue de agrupamiento. Los animales capturados se encontraban en un área total de 581.12 km2 cubierta por un 78% de manglares y playas y un 22% por hábitats modificados. Comparando la cobertura vegetal de 1992 y 2000, nuestros resultados mostraron baja densidad poblacional asociada a la reducción de hábitat. Las diferencias en la ecología poblacional entre los sitios continentales y los insulares sugieren que un programa de monitoreo a largo plazo del Cocodrilo Americano permite distinguir entre las fluctuaciones naturales y los cambios antropogénicos sobre la dinámica poblacional y el estado de conservación.
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