New clues on anuran evolution: the oldest record of an extant hyloid clade in the Oligocene of Patagonia

Despite the enormous diversity of the extant South American batrachofauna, its fossil record is sparse. Few pre-Neogene anuran remains have been attributed to extant taxa and, although some have been considered neobatrachians their relationships with extant groups are still mostly uncertain. In this context, a series of fossils recently collected in Oligocene sediments of central Patagonia are assigned to Odontophrynidae. This assignation is supported by an exclusive combination of characters, including extensive frontoparietals, in medial contact and deflecting posteriorly, with crescent-shaped posterolateral projections; robust pterygoid anterior ramus, reaching the planum antorbitale, projecting dorsally; notched premaxillary pars palatine; dentate vomers, narrowly separated medially; robust neopalatines, narrowly separated medially, bearing a conspicuous ridge, and with expanded lateral edges. The well-preserved fossil specimens were considered representative of a new genus and species, Chachaiphrynus lynchi. The presence of an Oligocene Odontophrynidae in central Patagonia, about 500 km south from the southern-most extant distribution of the group, would be associated with the more benign climate inferred in this region during the Paleogene. At the same time, this record represents the single pre-Neogene certain record of an extant clade deeply nested in Hyloidea, providing an exceptional high-quality calibration point to temporally frame the anuran phylogeny.

http://www.zoobank.org/urn:lsid:zoobank.org:act:AA043DC2-BCA5-4301-8FB0-FEB56B0F4404     

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.     

A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia,Argentina

The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500‐km²‐area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole‐genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. admixture and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in the expression of phytochrome signalling genes. Pat had higher PIF3 and PIF5 and lower HY5 expression under Rc light; and lower expression of PIL1, ATHB2 and HFR1 under shade compared to Col‐0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparison with other introduced populations will provide additional information for association studies and allow for a more detailed assessment of the demographic events following colonization.     

Marine and continental synchronous climatic records: Towards a revision of the European Mid-Miocene mammalian biochronological framework

The Middle Miocene climatic cooling (MCC) is a global event recorded synchronously in the marine and continental realms by several geo- and bioindicators around 15-13.5 Ma. The temporal distribution of European plants and ectothermic vertebrates indicates a similar response to the MCC around 15-13.5 Ma. According to the existing correlations of the European mammalian biochronological time scale to the Geomagnetic Polarity Time Scale (GPTS), a cenogram analysis revealed an important reorganisation of the Middle Miocene European terrestrial mammalian faunas that seems to take place later, around 11.5-11 Ma. This discrepancy between the timing of faunal changes can be solved by considering the recent biochronological and magnetostratigraphic data leading to reinterpretations of the debated ages of several Middle Miocene localities that need to be placed before the MCC event.     

Attitudes of local people towards conservation and alternatives to forest resources: A case study from the lower Himalayas

This paper examines the attitudes of local people living in and around the forest corridor linking the Rajaji and Corbett National Parks, northern India. Door to door surveys were carried out, and using fixed response questionnaires people were interviewed to examine their views towards conservation and proposed alternatives to the forest resources for reducing biomass demand from the forest. The study revealed that in the area the concept of conservation of forests is well supported. Nevertheless, people are extracting biomass from the corridor forest for their sustenance. The dependence of the people on the forest is due to lack of alternatives to the forest resources, inability of the people to produce alternatives from market, and in some cases it is habitual or traditional. In a situation where forest resources will not be available, people without any alternatives to forest resources are ready to agitate against such rules. People who oppose such decisions are not always dependent on the corridor forest but are antagonistic towards the forest department and want to use this opportunity to retaliate by stealing from the forest. The former category of people are the ones for whom income generating activities would be important while the later category should be the targets of extension programs designed to establish permanent lines of dialogue with the forest department. To some extent human-animal conflict and apathetic attitude of the forest department are also responsible for antagonism of people.     

Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland

Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500–1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (N_E), a marked bottleneck event at 1400–1500 and a decrease in N_E in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.     

Brief communication: Ancient nuclear DNA and kinship analysis: the case of a medieval burial in San Esteban Church in Cuellar (Segovia, Central Spain)

The aim of this work was to investigate a very common situation in the archaeological and anthropological context: the study of a burial site containing several individuals, probably related genetically, using ancient DNA techniques. We used available ancient DNA and forensic protocols to obtain reliable results on archaeological material. The results also enabled molecular sex determination to be compared with osteological data. Specifically, a modified ancient DNA extraction method combined with the amplification of nuclear markers with the AmpFlSTR®MiniFiler? kit(Applied Biosystems) was used. Seven medieval individuals buried in four niches dated in the 15th Century at San Esteban Church in Cuellar (Segovia, Central Spain) were analyzed by the proposed method, and four of seven provided complete autosomal short tandem repeat (STRs) profiles. Kinship analyses comprising paternity and sibship relations were carried out with pedigree‐specific software used in forensic casework. A 99.98% paternity probability was established between two individuals, although lower percentages (68%) were obtained in other cases, and some hypothetical kinship relations were excluded. The overall results could eventually provide evidence for reconstructing the historical record. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.     

A hierarchical ecological classification system along the NE Atlantic coast: focusing on the local scale (Cantabria,N Spain)

An ecological classification at the local scale may be a useful tool for conservation planning and for the implementation of specific management programmes in a region. For this purpose, a methodology previously applied on a small scale has been adapted to classify the coast of Cantabria (N Spain). This methodology includes a physical classification and biological validation. The shoreline was divided into 1 km stretches, and the abiotic variables (sea surface temperature, photosynthetically active radiation, significant wave height and coastal morphology) were recorded for each stretch. A hierarchical classification was proposed, with a first level that encompassed a grouping of quantitative variables based on SOM and k-mean analysis and a second level that subdivided the previous groups according to the categorical variable ‘coastal morphology’. To validate the classification using biological data, cover of intertidal macroalgal species was obtained at 14 sites along the study area, and several statistical analyses were applied to test the ecological significance of this classification. Three physical units were obtained (western (W), central (C) and eastern (E) coast), based on abiotic variables. Each group was then subdivided into subunits according to its coastal morphology (cliffs or wave-cut platforms). A general agreement between the macroalgal distribution and physical units was accomplished. In the lower intertidal, Bifurcaria bifurcata and Halopteris scoparia dominated the western and central areas, whereas Corallina spp./Ellisolandia elongata and Gelidium spp. were most abundant towards the east. In contrast, throughout the middle intertidal, Corallina. spp./E. elongata were the dominant taxa. The classification system developed in this study completes a hierarchical framework for classifying the NE Atlantic coast, a promising approach that permits the application of the most suitable resolution in each case study that could be applicable to a wide range of coastal areas.     

Anthropocene invasion of an ecosystem engineer: resolving the history of Corophium volutator (Amphipoda: Corophiidae) in the North Atlantic

Resolving the natural histories of species is important for the interpretation of ecological patterns, as it provides evolutionary context for the interactions between organisms and their environment. Despite playing an integral role on the intertidal mudflats of the North Atlantic as an abundant food source for predators and as an ecosystem engineer that alters the soft sediment environment, no previous studies have provided empirical evidence to determine the biogeographical origin of the amphipod Corophium volutator. To resolve its status as introduced or indigenous in Europe and North America, we analyzed sequence data for two mitochondrial loci and two nuclear markers, aiming to determine whether the present range of C. volutator is the result of unresolved taxonomy, persistence in glacial refugia, natural trans‐Atlantic dispersal, or human‐mediated introduction. Our results demonstrate a reduced genetic diversity in North American populations that is a subsample of diversity in European populations, with coalescent analyses of mitochondrial and nuclear DNA supporting different models of multiple introductions from Europe to the Bay of Fundy and Gulf of Maine in North America. These results suggest that C. volutator was introduced to North America prior to the first surveys of local biota in the 20th Century, which has broad implications for interpretations of community and ecosystem interactions in the North Atlantic intertidal. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 288–304.     

Population origins in Mongolia: genetic structure analysis of ancient and modern DNA

In the present study, nuclear (autosomal and Y-chromosome short tandem repeats) and mitochondrial (hypervariable region I) ancient DNA data previously obtained from a 2,300-year-old Xiongnu population of the Egyin Gol Valley (south of Lake Baikal in northern Mongolia) (Keyser-Tracqui et al. 2003 Am. J. Hum. Genet. 73:247-260) were compared with data from two contemporary Mongolian populations: one from the same location (Egyin Gol Valley plus a perimeter of less than 100 km around the valley), and one from the whole of Mongolia. The principal objective of this comparative analysis was to assess the likelihood that genetic continuity exists between ancient and present-day Mongolian populations. Since the ancient Xiongnu sample might have been composed of some of the ancestors of the present-day Yakuts, data from a present-day Yakut population, as well as published data from Turkish populations, were also included in the comparative analysis. The main result of our study was the genetic similarity observed among Mongolian samples from different periods and geographic areas. This result supports the hypothesis that the succession over time of different Turkic and Mongolian tribes in the current territory of Mongolia resulted in cultural rather than genetic exchanges. Furthermore, it appears that the Yakuts probably did not find their origin among the Xiongnu tribes, as we previously hypothesized.     

From subsistence to market: A case study of the mbuti net hunters

This article describes the recent transition from subsistence to market hunting of some net-hunting Mbuti, a nomadic society of the Ituri Forest of Zaire. The history of this development dates to the late 1950s, as the Mbuti began to have increasing contact with commercial meat traders, called bachuuzi, from outside markets. Before this, the Mbuti had a long history of contact with local swidden agriculturalists, called bakbala, a relationship that continues today. It is sanctioned by religious beliefs, but material exchanges are also important. The Mbuti provide bakbala with meat and other forest resources and receive in return iron implements, tobacco, and cultivated food. The Mbuti view such items now as necessities; however, this does not allow the bakbala to subjugate or control them. Most exchanges take place in the bakbala's village at the Mbuti's discretion, and exchange rates are not fixed. Finally it appears that such trade does not undermine the resource base of either group. The Mbuti's commercial exchanges contrast with this subsistence-oriented system. Unlike the bakbala, the bachuuzi traders establish themselves in the Mbuti's forest camps, where they can promote intensified net hunting and monopolize trade of meat. The Mbuti tolerate the alien traders in camp because they are often a convenient source of food and other desired material goods; however, they do not share the traders' commercial motives. The Mbuti freely manipulate credit to their own advantage and they are often able to evade the traders' efforts at economic control. The future of market hunting is uncertain. Mbuti material needs are changing and the antelope fauna (Cephalophinae) upon which commercial trade depends is being reduced in some areas.A fellowship from the Thomas J. Watson Foundation provided financial support for this research. I am also thankful to Citoyen Bokanga Ekanga Botombele, Commissaire d'Etat du Zaire for his interest in my work and support in obtaining necessary visas, and to Père Thyert of the Catholic Mission of Biambwe for his generous hospitality. Terese Butler Hart, Colin Turnbull, Paul Riesman, Randall Packard, Paul Wholt, and Stuart Marks criticized drafts of this paper. Finally, I am most grateful to the Mbuti with whom I lived for so generously sharing their daily life with me.     

Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath hen

Population introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens.     

The human genome project: Towards an analysis of the empirical,ethical, and conceptual issues involved

In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the project. The second section distinguishes among four kinds of issues relevant to an evaluation of the HGP: those economic and organizational issues related to the feasibility of the project; the ethical questions arising in the development of the project and the application of the data gathered; the empirical issues relevant to the scientific value of the project; and conceptual issues like reductionism and determinism relevant to understand the nature and scope of the project. In a third section, I analyze in detail whether the HGP and, more generally, molecular biology is reductionistic.     

The application of RAPD markers in stock discrimination of the four-wing flyingfish, Hirundichthys affinis in the central western Atlantic

The polymerase chain reaction–random amplified polymorphic DNA (PCR–RAPD) technique was used to examine genetic variability and population structuring in the four-wing flyingfish, Hirundichthys affinis within the central western Atlantic. Three random decamer primers and pairs of these primers were used to amplify nuclear DNA from 360 fish sampled from six populations (at five locations) across the region. A total of 58 polymorphic RAPD markers were identified, 20 of which were population-specific and six of which were subregional or stock-specific markers. Cluster analysis of similarity indices indicated the presence of three genetically distinct subregional stocks located in the eastern Caribbean, southern Netherlands Antilles and Brazil, respectively. Estimates of gene diversity (φ) and gene flow ( Nm ) are consistent with this three-stock hypothesis. Furthermore, partially restricted gene flow was apparent among spatially and temporally separate sampled populations within the eastern Caribbean subregional stock, indicating the possible presence of different spawning groups. These results are entirely consistent with those obtained from PCR–RFLP analysis of the mtDNA D-loop in the same fish, indicating the presence of barriers to dispersal and interbreeding in both sexes. We conclude that the PCR–RAPD technique is suitable for determining population stock structure in this species and that a three-stock approach to managing H. affinis within the central western Atlantic would be appropriate.     

A conceptual framework for understanding the perspectives on the causes of the science–practice gap in ecology and conservation

Applying scientific knowledge to confront societal challenges is a difficult task, an issue known as the science–practice gap. In Ecology and Conservation, scientific evidence has been seldom used directly to support decision‐making, despite calls for an increasing role of ecological science in developing solutions for a sustainable future. To date, multiple causes of the science–practice gap and diverse approaches to link science and practice in Ecology and Conservation have been proposed. To foster a transparent debate and broaden our understanding of the difficulties of using scientific knowledge, we reviewed the perceived causes of the science–practice gap, aiming to: (i) identify the perspectives of ecologists and conservation scientists on this problem, (ii) evaluate the predominance of these perspectives over time and across journals, and (iii) assess them in light of disciplines studying the role of science in decision‐making. We based our review on 1563 sentences describing causes of the science–practice gap extracted from 122 articles and on discussions with eight scientists on how to classify these sentences. The resulting process‐based framework describes three distinct perspectives on the relevant processes, knowledge and actors in the science–practice interface. The most common perspective assumes only scientific knowledge should support practice, perceiving a one‐way knowledge flow from science to practice and recognizing flaws in knowledge generation, communication, and/or use. The second assumes that both scientists and decision‐makers should contribute to support practice, perceiving a two‐way knowledge flow between science and practice through joint knowledge‐production/integration processes, which, for several reasons, are perceived to occur infrequently. The last perspective was very rare, and assumes scientists should put their results into practice, but they rarely do. Some causes (e.g. cultural differences between scientists and decision‐makers) are shared with other disciplines, while others seem specific to Ecology and Conservation (e.g. inadequate research scales). All identified causes require one of three general types of solutions, depending on whether the causal factor can (e.g. inadequate research questions) or cannot (e.g. scientific uncertainty) be changed, or if misconceptions (e.g. undervaluing abstract knowledge) should be solved. The unchanged predominance of the one‐way perspective over time may be associated with the prestige of evidence‐based conservation and suggests that debates in Ecology and Conservation lag behind trends in other disciplines towards bidirectional views ascribing larger roles to decision‐makers. In turn, the two‐way perspective seems primarily restricted to research traditions historically isolated from mainstream conservation biology. All perspectives represented superficial views of decision‐making by not accounting for limits to human rationality, complexity of decision‐making contexts, fuzzy science–practice boundaries, ambiguity brought about by science, and different types of knowledge use. However, joint knowledge‐production processes from the two‐way perspective can potentially allow for democratic decision‐making processes, explicit discussions of values and multiple types of science use. To broaden our understanding of the interface and foster productive science–practice linkages, we argue for dialogue among different research traditions within Ecology and Conservation, joint knowledge‐production processes between scientists and decision‐makers and interdisciplinarity across Ecology, Conservation and Political Science in both research and education.     

Colonization and divergence: phylogeography and population genetics of the Atlantic coast beach mice

Barrier island taxa provide an opportunity to investigate recent evolutionary processes, such as colonization and isolation of recently diverged taxa, and provide important insights into understanding contemporary diversity and the assessment of conservation units. Using rapidly evolving genetic markers (mitochondrial DNA and microsatellites), we studied the Atlantic coast beach mouse subspecies (Peromyscus polionotus decoloratus, P. p. niveiventris, and P. p. phasma). Our data indicate that each of the extant coastal subspecies (P. p. niveiventris and P. p. phasma) is comprised of unique haplotypes indicative of their isolation, while the extinct subspecies, P. p. decoloratus, contain a single haplotype, which was shared with P. p. phasma. Moreover, all the coastal haplotypes originate from a single mainland haplotype found in central Florida, USA. The microsatellite data indicated high levels of genetic structure among our sampled populations. Additionally, these data group the populations into three distinct genetic clusters, with each of the extant coastal subspecies belonging to their own cluster and the mainland individuals forming a separate cluster. The extant Atlantic coast beach mice are on separate evolutionary trajectories, thus representative of separate taxonomic units. Therefore, the data support that two extant subspecies on the Florida Atlantic coast fit the Distinct Population Segment designation and should be managed and conserved as two separate independent units.     

Molecular characterisation and development of rapid molecular methods to identify species of Gracilariaceae from the Atlantic coast of Morocco

In Gracilariaceae, species identification is traditionally based on gross morphology; therefore the taxonomic status of terete individuals remains frequently problematic due to the lack of diagnostic characters to identify specimens. Different morphospecies have been recorded along the Atlantic coast of Morocco; however, no clear diagnostic characters were available to discriminate between terete species. Rapid molecular techniques have been developed recently to resolve many taxonomic problems and to re-assess the global diversity and biogeography in algae. In this study, molecular markers were used as DNA barcoding to characterise species. The sequence of the Rubisco spacer allowed identification of six species of Gracilariaceae: Gracilaria gracilis, Gracilaria dura, Gracilaria conferta, Gracilaria vermiculophylla, Gracilaria multipartita and Gracilariopsis longissima. In order to identify species with certainty, two simple and rapid methods based on the amplification of rDNA ITS and PCR-RFLP of the large subunit of the Rubisco were developed.