Is dispersal guided by the environment? A comparison of interspecific gene flow estimates among differentiated regions of a newt hybrid zone

How frequently genes pass through a hybrid zone may be influenced by the environment. Accordingly, in long hybrid zones that span more than one environmental setting, different patterns may emerge. The varied conditions allow testing of hypotheses on dispersal as a function of the environment. We reconstruct the amount and direction of gene flow across a heterogeneous hybrid zone of two species of marbled newts (Triturus marmoratus and Triturus pygmaeus), in four widely separated areas of the Iberian Peninsula from one mitochondrial and three nuclear genes. The main variables associated with the position of the contact zone are precipitation, rivers, altitude and relief. In some sections of the contact zone, however, its position is not correlated with any environmental factor and is instead determined by the shortest geographical distance between fixed positions at either side (mountains in the East and river in the West). In areas where the position of the zone is stable, gene flow was bidirectional. External data show that T. pygmaeus has superseded T. marmoratus over a large area and here gene flow was unidirectional. The prediction that a major river would reduce gene flow was not confirmed.     

Occurrence of Three Felids across a Network of Protected Areas in Thailand: Prey,Intraguild, and Habitat Associations

Clouded Leopard, Leopard, and Tiger are threatened felids in Southeast Asia, but little is known about the factors influencing their distributions. Using logistic regression, we assessed how habitat variables, prey detection patterns, and presence of intraguild predators affect the occurrence of these felids across 13 protected areas within Thailand. Our analysis is based on data from 1108 camera‐trap locations (47,613 trap‐nights). Clouded Leopard and Leopard are associated with habitat where Red Muntjac and Eurasian Wild Pig were most likely to be present. Tiger are associated with habitat with a higher likelihood for the presence of Gaur, Eurasian Wild Pig, and Sambar. Clouded Leopard and Tiger were both weakly associated with areas with mature evergreen forest. Besides availability of prey, associations with potential competitors also appear to influence the distribution of these felids, although the strength of these effects requires further investigation. Occurrence rates for Clouded Leopard were no different in protected areas with Leopard versus without Leopards. Leopard had similar occurrence rates regardless of the presence of Tiger, but Leopards were less likely to be detected at the same camera‐trap points with the larger felid. Our results suggest that the two most commonly photographed prey species in the study areas serve as key prey species, Eurasian Wild Pig for all three carnivores and Red Muntjac for Leopard and Clouded Leopard.     

Relationships among fourteen species of Satureja growing wild in Iran detected with molecular markers

The genus Satureja is an important plant with a number of aromatic and medicinal properties. In this research, the relative efficiencies of amplified fragment length polymorphism (AFLP) and selectively amplified microsatellite polymorphic loci (SAMPL) were used to detect genetic relationships among 14 species of Satureja, growing wild in Iran. Eleven AFLP and 14 SAMPL primer combinations produced 999 and 1142 scorable bands, respectively, all of the fragments of which were found to be polymorphic. The average genetic similarity values based on Jaccard's coefficient were 0.24 and 0.21 for AFLP and SAMPL, respectively, indicating considerable distance and diversity in the studied germplasm. The correlation coefficients were statistically significant between both marker systems (r = 0.89). UPGMA derived from the combined binary data matrices of both markers depicted genetic distinctions among the studied species and clustered them into two main clusters and several groups. S. edmondi showed the maximum distance from other species and was placed into a single main cluster, while the maximum similarity was obtained between S. rechingeri and S. khuzistanica. Our results indicate that both marker systems are suitable for differentiating individuals and species of this genus.     

Assisted reproductive technologies in captive rhinoceroses

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Mycorrhizal specificity does not limit the distribution of an endangered orchid species

What factors determine the distribution of a species is a central question in ecology and conservation biology. In general, the distribution of plant species is assumed to be controlled by dispersal or environmentally controlled recruitment. For plant species which are critically dependent on mycorrhizal symbionts for germination and seedling establishment, specificity in mycorrhizal associations and availability of suitable mycorrhizal fungi can be expected to have a major impact on successful colonization and establishment and thus ultimately on a species distribution. We combined seed germination experiments with soil analyses and fungal assessments using 454 amplicon pyrosequencing to test the relative importance of dispersal limitation, mycorrhizal availability and local growth conditions on the distribution of the orchid species Liparis loeselii, which, despite being widely distributed, is rare and endangered in Europe. We compared local soil conditions, seed germination and mycorrhizal availability in the soil between locations in northern Belgium and France where L. loeselii occurs naturally and locations where conditions appear suitable, but where adults of the species are absent. Our results indicated that mycorrhizal communities associating with L. loeselii varied among sites and plant life cycle stages, but the observed variations did not affect seed germination, which occurred regardless of current L. loeselii presence and was significantly affected by soil moisture content. These results indicate that L. loeselii is a mycorrhizal generalist capable of opportunistically associating with a variety of fungal partners to induce seed germination. They also indicate that availability of fungal associates is not necessarily the determining factor driving the distribution of mycorrhizal plant species.     

Prehistoric and historic distributions of the critically endangered Mediterranean monk seal (Monachus monachus) in the eastern Atlantic

The present Atlantic range of the Mediterranean monk seal (Monachus monachus), a critically endangered species, comprises two populations in the Desertas Islands and Cape Blanco region. The species is currently the subject of an action plan that encourages the recolonization of its former range. I investigated their causes of its disappearance using species records from paleo‐archeological sites and historical sightings/toponyms. I hypothesize that the species' prehistoric range extended from the continental coasts of North Africa to the Iberian Peninsula, an area larger than its current known range. It is further hypothesized that the historic range included at least 13 colonies, seven more than the present number; and that the original optimal breeding habitat was open beaches, while sea caves were a suboptimal, marginal habitat. It is suggested that hunting and the disappearance of two islands due to a historical tsunami event explain the disappearance of the other populations, leaving only those at the Desertas Islands and Cape Blanco that were sheltered in sea caves. Furthermore, the use of sea caves, in conjunction with effective legal protection in the 20th century, explains the present‐day survival of these Atlantic colonies of M. monachus.     

Comprehensive DNA barcoding of the herpetofauna of Germany

We present the first comprehensive DNA barcoding study of German reptiles and amphibians representing likewise the first on the European herpetofauna. A total of 248 barcodes for all native species and subspecies in the country and a few additional taxa were obtained in the framework of the projects ‘Barcoding Fauna Bavarica’ (BFB) and ‘German Barcode of Life’ (GBOL). In contrast to many invertebrate groups, the success rate of the identification of mitochondrial lineages representing species via DNA barcode was almost 100% because no cases of Barcode Index Number (BIN) sharing were detected within German native reptiles and amphibians. However, as expected, a reliable identification of the hybridogenetic species complex in the frog genus Pelophylax was not possible. Deep conspecific lineages resulting in the identification of more than one BIN were found in Lissotriton vulgaris, Natrix natrix and the hybridogenetic Pelophylax complex. A high variety of lineages with different BINs was also found in the barcodes of wall lizards (Podarcis muralis), confirming the existence of many introduced lineages and the frequent occurrence of multiple introductions. Besides the reliable species identification of all life stages and even of tissue remains, our study highlights other potential applications of DNA barcoding concerning German amphibians and reptiles, such as the detection of allochthonous lineages, monitoring of gene flow and also noninvasive sampling via environmental DNA. DNA barcoding based on COI has now proven to be a reliable and efficient tool for studying most amphibians and reptiles as it is already for many other organism groups in zoology.     

Geographic characteristics of sable (Martes zibellina) distribution over time in Northeast China

Understanding historical context can help clarify the ecological and biogeographic characteristics of species population changes. The sable (Martes zibellina ) population has decreased dramatically in Northeast China since the l950s, and understanding the changes in its distribution over time is necessary to support conservation efforts. To achieve this goal, we integrated ecological niche modeling and historical records of sables to estimate the magnitude of change in their distribution over time. Our results revealed a 51.71% reduction in their distribution in 2000–2016 compared with the potential distribution in the 1950s. This reduction was related to climate change (Pearson's correlation: Bio1, ?.962, p  < .01; Bio2, ?.962, p  < .01; Bio5, .817, p  < .05; Bio6, .847, p  < .05) and human population size (?.956, p  < .01). The sable population tended to migrate in different directions and elevations over time in different areas due to climate change: In the Greater Khingan Mountains, they moved northward and to lower elevations; in the Lesser Khingan Mountains, they moved northward; and in the Changbai Mountains, they move southward and to higher elevations. Active conservation strategies should be considered in locations where sable populations have migrated or may migrate to.     

Genetic structure and preservation strategies of autochthonous vegetable crop landraces of north‐western Italy

A number of horticultural crop landraces are still grown in Piedmont (NW Italy), despite the dominance of improved cultivars and hybrids. Conservation strategies, both in an ex situ and an in situ context are required to prevent their loss. Here we describe an AFLP‐based assessment of the genetic structure of leek, garlic, celery, red beet, cultivated cardoon, sweet pepper and common bean autochthonous landraces. Each landrace was sampled by selecting 3–5 populations representative of the area of cultivation. The genotypic data showed that the crop's breeding system was less important for determining genetic structure than the selection criteria adopted by the producers, the extent of informal seed exchange among producers and natural selection imposed by the local environmental conditions. The genotypic data identified alleles which were common, some which were restricted to a particular locality and some which were either infrequent or rare. On this basis, the most representative population(s) for each landrace were recognised and targeted for conservation. The landraces in study differed markedly from one another with respect to their genetic structure, and so they may represent an appropriate reference model for the management of crop landraces grown in fragmented areas and at risk of genetic erosion or extinction.     

Genetic structure of two Prosopis species in Chaco areas: A lack of allelic diversity diagnosis and insights into the allelic conservation of the affected species

The Gran Chaco is the largest continuous region of the South American dry forest, spanning Argentina, Paraguay, Bolivia, and Brazil. Prosopis rubriflora and Prosopis ruscifolia are typical tree species of chaquenian area forests, which have been subjected to continuous fragmentation caused by cattle raising. This study evaluated P. rubriflora and P. ruscifolia in areas with varying levels of disturbance. We investigated the contemporary genetic diversities of both species in areas with distinct anthropogenic disturbances. Even with a lower heterozygote frequency, disturbed areas can provide important storage for alleles, allowing the maintenance of diversity. The genetic diversity of P. rubriflora was surprisingly similar to that of P. ruscifolia (H_e = 0.59 and H_e = 0.60, respectively) even with very different distribution ranges of both species. However, P. ruscifolia exhibited a higher intrapopulation fixation index than P. rubriflora. P. rubriflora showed evidence of bottlenecking in 64% of the sampled areas, while P. ruscifolia showed such evidence in 36% of the sampled areas. Additionally, P. rubriflora had two distinct populations due to its disjunctive geographic distribution, whereas P. ruscifolia had a single population that exhibited few signs of population structure in some areas, possibly due to the main pollinators presenting a short range of dispersion. Our results suggest that 42 Chaco areas should be conserved to retain the minimum of 500 individuals necessary to maintain genetic diversity for 100–1,000 generations. This study improves our understanding of these two Prosopis species and provides information for the conservation of their genetic diversities.     

Colonization and extinction dynamics of a declining migratory bird are influenced by climate and habitat degradation

Uncovering the mechanisms involved in the decline of long‐distance migrants remains one of the most pressing issues in European conservation. Since the 1980s, the British breeding population of Garden Warbler Sylvia borin has declined by more than 25%. Here we use data from repeated bird surveys of woodland sites in the 1980s and in 2003–2004 to show that, although the overall population declined between the two periods, the probability of occupancy for this species increased at high latitudes and decreased at low latitudes. Range shifts such as this arise from a change in the ratio of colonizations to extinctions at the range margins, and we therefore related colonization and local extinction at the patch level to concurrent changes in temperature and habitat. The probability of patch colonization by this species was significantly lower where the percentage cover of vegetation in the understorey had declined, reducing habitat quality for this species. The probability of local extinction was significantly correlated with increasing mean May temperature, which may reflect a change in phenology, making breeding conditions less suitable. Changed regimes of grazing and woodland management could be used to increase habitat suitability and thereby increase colonization probability at the local scale, which may in turn increase the probability of patch occupancy despite future climatic unsuitability.     

Subspecies delineation amid phenotypic,geographic and genetic discordance in a songbird

Understanding the processes that drive divergence within and among species is a long‐standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra‐ and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced‐representation sequencing approach to generate a panel of 1929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish–water marsh habitats. These patterns support the current species‐level recognition but do not match the subspecies‐level taxonomy within each species—a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.     

Morphometric and genetic differentiation among populations of flat‐headed cusimanse (Crossarchus platycephalus) in Nigeria

Geographic barriers can partition genetic diversity among populations and drive evolutionary divergence between populations, promoting the speciation process and affecting conservation goals. We integrated morphological and genomic data to assess the distribution of variation in the flat‐headed cusimanse (Crossarchus platycephalus), a species of least conservation concern, on either side of the River Niger in Nigeria. Ecological disturbances affect the conservation status of many other animals in this region. The two populations were differentiated in the snout and fore limbs, with greater morphological diversity in the western population. We used Restriction site Associated DNA sequencing (RAD‐seq) and identified two genotypic clusters in a STRUCTURE analysis. Individuals from the eastern population are almost entirely assigned to one cluster, whereas genotypes from the western population are a mixture of the two clusters. The population from west of the River Niger also had higher heterozygosity. The morphological and population genetic data are therefore in agreement that the population from west of the River Niger is more diverse than the eastern population, and the eastern population contains a subset of the genetic variation found in the western population. Our results demonstrate that combining morphological and genotypic measures of diversity can provide a congruent picture of the distribution of intraspecific variation. The results also suggest that future work should explore the role of the River Niger as a natural barrier to migration in Nigeria.