Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog

The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution.     

Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin

Although many studies have documented the effect of glaciation on the evolutionary history of Northern Hemisphere flora and fauna, this study is the first to investigate how the indirect aridification of Africa caused by global cooling in response to glacial cycles at higher latitudes has influenced the evolutionary history of an African montane bird. Mitochondrial DNA sequences from the NADH 3 gene were collected from 283 individual Starred Robins (Pogonocichla stellata, Muscicapoidea). At least two major vicariant events, one that separated the Albertine Rift from all but the Kenyan Highlands around 1.3-1.2 Myrs BP, and another that separated the Kenyan Highlands from the northern Eastern Arc, and the northern Eastern Arc from the south-central Eastern Arc between 0.9 and 0.8 Myrs BP appear to underlie much of the observed genetic diversity and structure within Starred Robin populations. These dates of divergence suggest a lack of recurrent gene flow; although the Albertine Rift and south-central Eastern Arc share haplotypes, based on coalescent analyses this can confidently be accounted for by ancestral polymorphism as opposed to recurrent gene flow. Taken collectively, strong evidence exists for recognition of four major ancestral populations: (1) Kenyan Highlands (subspecies keniensis), (2) Albertine Rift (ruwenzori), (3) northern Eastern Arc (helleri), and (4) south-central Eastern Arc, Ufipa and the Malawi Rift (orientalis). The estimated divergence times cluster remarkably around one of the three estimated peaks of aridification in Africa during the Plio-Pleistocene centred on 1 Myrs BP. Further, time to most recent common ancestor (TMRCA) estimates (1.7-1.6 Myrs BP) of gene divergence between the Albertine Rift and the other montane highlands corresponds closely with a second estimated peak of aridification at about 1.7 Myrs BP. Collectively, these results suggest that aridification of Africa in response to glaciation at higher latitudes during the Pleistocene has had a profound influence on montane speciation in east and central Africa.     

Smallholder Livelihoods,Wealth and Deforestation in the Eastern Amazon

In this paper, I examine patterns of wealth accumulation and their influence on deforestation among smallholders at Uruará and Redenção, in the state of Pará in the Brazilian Eastern Amazon. I argue that the development of the smallholder economy has not been a linear process, and the diversity of smallholder farming systems and their patterns of wealth accumulation have varied implications for the rate and magnitude of deforestation. However, whilst there are differential impacts of farming practices on deforestation—cattle ranching has a greater impact than cash cropping or subsistence agriculture—the stronger correlate of deforestation is the wealth of the farmers. Wealthier farmers not only tend to deforest more in absolute terms, but also show a slightly greater propensity to deforest whatever their production system. Though cattle production is a key driver of wealth accumulation and thus deforestation, a significant number of smallholders adopt diversified production systems. The main factors explaining the relationship between the farming systems and deforestation were years of residence on the lot, distance of the lot to main market and the amount of day labor hired—and not variables describing household structure.     

New insights into the genetic diversity of zooxanthellae in Mediterranean anthozoans

Symbiotic dinoflagellates of the genus Symbiodinium, also called zooxanthellae, are found in association with a wide diversity of shallow-water anthozoans. The Symbiodinium genus includes numerous lineages, also referred to as clades or phylotypes, as well as a wide diversity of genetic sub-clades and sub-phylotypes. There are few studies characterizing the genetic diversity of zooxanthellae in Mediterranean anthozoans. In this study, we included anthozoans from the Western Mediterranean Sea and by means of internal transcriber (ITS) and large sub-unit (LSU) rRNA markers we corroborate what has been previously identified, demonstrating that phylotype “Temperate A” is very common among host Cnidaria in this basin. Our finding of fixed differences in ITS and LSU markers that correspond to different host taxa, indicate that this clade may comprise several closely-related species. Previous studies have reported the occurrence of Symbiodinium psygmophilum (formerly sub-clade B2) associated with Oculina patagonica and Cladocora caespitosa in the Eastern Mediterranean. Here, we identify this association in O. patagonica from the Western Mediterranean but not in C. caespitosa, suggesting some differences in symbiotic combinations between the Western and Eastern Mediterranean Basins.     

Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles

The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.     

THE ZOOGEOGRAPHY AND CENTERS OF ORIGIN OF THE CRAYFISH SUBGENUS PROCERICAMBARUS (DECAPODA: CAMBARIDAE)

The Central Highlands region in the central United States is a taxonomically diverse region with a high incidence of stream endemism. Based on the distributions of the diverse ichthyofauna in the region, a pre-Pleistocene pattern of diversity due to vicariant events has been proposed to explain high levels of endemism and species richness. We tested this hypothesis using crayfish phylogenies and distributional patterns for species distributed in the Central Highlands region. We concluded that both pre-Pleistocene and Pleistocene hypotheses are compatible with the crayfish distributions and these distributions are likely due to a combination of both vicariant and dispersal events. Furthermore, we suggest a Pleistocene center of origin for the crayfish subgenus Procericambarus within the Ozark region and a pre-Pleistocene center of origin for the genus Orconectes within the Eastern Highlands region.     

Distribution and importance of the lichen vegetation of the Scottish Highlands

Summary

The mountains of the Western Highlands of Scotland support a lichen vegetation that is apparently unique in Europe, and probably the world. This lichen vegetation consists mainly of microlichens and is important both intrinsically, with a number of rare and apparently endemic taxa and communities, and as a major contributor to the botanical biodiversity of the ecosystem. By contrast, the lichen vegetation of the Eastern Highlands, which consists mostly of terricolous macrolichens, is best considered a fragmented, species-poor outlier of that present in Scandinavia and is of national interest only.     

Intraspecific phylogeography of Percina evides (Percidae: Etheostomatinae): an additional test of the Central Highlands pre-Pleistocene vicariance hypothesis

North America exhibits the most diverse freshwater fish fauna among temperate regions of the world. Species diversity is concentrated in the Central Highlands, drained by the Mississippi, Gulf Slope and Atlantic Slope river systems. Previous investigations of Central Highlands biogeography have led to conflicting hypotheses involving dispersal and vicariance to explain the diversity and distribution of the freshwater fish fauna. In this investigation predictions of the Central Highlands pre-Pleistocene vicariance hypothesis are tested with a phylogeographic analysis of the percid species Percina evides, which is widely distributed in several disjunct areas of the Central Highlands. Phylogenetic analysis of complete gene sequences of mitochondrially encoded cytochrome b recover three phylogroups, with very low levels of sequence polymorphism within groups. The two western phylogroups are monophyletic with respect to the eastern phylogroup. The recovery of two monophyletic lineages with an eastern and western distribution in the disjunct highland areas is a pattern expected from vicariance, but is not predicted by the Central Highlands pre-Pleistocene vicariance hypothesis. The recovery of very limited mitochondrial DNA polymorphism and lack of phylogeographic structuring across the entire range of the eastern clade, very shallow polymorphism between the disjunct Missouri River and upper Mississippi River populations, and lack of sequence polymorphism in the upper Mississippi River populations, support a hypothesis of dispersal during or following the Pleistocene. The present distribution of P. evides is best explained by both vicariant and dispersal events.     

Comparative study of spatial patterns and ecological niches of beetles in two Malaysian mountains elevation gradients

The study of beetle communities is a valuable approach for biogeographical and conservation studies because their species and ecological diversities are very high, and they take different roles in ecosystems. However, beetle macroecology and conservation studies are disproportionately scarce, especially in tropical Asia. The objective of this study is to compare beetle abundance, diversity and species richness along the elevation gradients in two mountains in Peninsular Malaysia. Three passive sampling methods were utilized for beetle sampling with four marked elevation gradients: 500 m, 1000 m, 1500 m and 1800 m. Species richness in Fraser’s Hill was higher at highest elevation, but this value was not-significantly different from these in other elevations, except for the site at 1000 m with significantly lower estimates. Genting Highlands showed a significant decrease in species richness with the increase in elevation, without differences between the higher elevation sites. Pairwise comparison of species richness, Simpson Dominance and Shannon diversity between same elevation sites of Fraser’s Hill and Genting Highlands were all significantly different. The levels of vertical and horizontal colonization have had comparatively different weights in terms of their effect on the pattern of diversity and the integration of the beetle community in these two localities. At Fraser’s Hill, similar conditions at different elevations drives different responses, whereas at Genting Highlands contrasting and different environmental conditions at each elevation, drives different responses. We suggest the potential use of these results for biodiversity conservation in terms of climate variables in accordance with niche patterns.     

The lichen vegetation associated with areas of late snow-lie in the Scottish Highlands

Abstract:The lichen vegetation associated with areas of late snow-lie in the Scottish Highlands is described and three lichen-dominated communities recognized; from the tops of large boulders, from small pebbles, and from damp soil. The first of these is exclusive to this habitat throughout the Highlands, whereas the other two are restricted to areas of late snow-lie in the Eastern Highlands but are of more widespread occurrence further west. The community from damp soil has affinities with the Solorinion croceae Klement, which occupies a similar ecological niche in Central Europe, but the two other communities are apparently undescribed. The importance of the eu-oceanic climate of the Western Highlands in determining the distribution of these communities is emphasized. The new combination Micarea cinerea f. tenuispora (D. Hawksw. & Poelt) Fryday is made for the anamorph of M. cinerea (Schaer.) Hedl.     

Dispersal, vicariance, and timing of diversification in Nothonotus darters

The species diversity of North American freshwater fishes is unparalleled among temperate regions of the planet. This diversity is concentrated in the Central Highlands of eastern North America and this distribution pattern has inspired different models involving either dispersal or vicariance to explain the high species diversity of North American fishes. The most popular of these models is the Central Highlands vicariance hypothesis (CHVH), which proposes an ancient and diverse widespread fauna that existed across a previously continuous highland landscape that is much different from today. The mechanisms of isolation in the CHVH involve specific instances of vicariance that affected several diverse lineages of Central Highlands fishes. We tested predictions of the CHVH and alternative models using a cytochrome b-inferred phylogeny of the darter clade Nothonotus. A Bayesian mixed-model method was used for phylogenetic analysis. The phylogenetic data set included all 20 recognized Nothonotus species, and most species were represented with multiple sequences. We were able to convert genetic branch lengths to absolute age using external fossil calibrations in the freshwater perciform fish clade Centrarchidae. Using a well-resolved Nothonotus phylogeny and divergence time estimates, we identify equal numbers of instances of both vicariance and dispersal among disjunct regions of the Central Highlands, biogeographic pseudocongruence, rather recent speciation in Nothonotus, and a surprisingly large amount of speciation within highland areas. With regard to Nothonotus, previous Central Highlands biogeographic models offer little in the way of providing possible mechanisms responsible for diversification in the clade. Patterns of speciation in Nothonotus are similar to those discovered in recent efforts that have included speciation as a parameter into classic models of island biogeography.     

Modelling range shifts and assessing genetic diversity distribution of the montane aquatic mayfly Ameletus inopinatus in Europe under climate change scenarios

Genetic diversity is one of the most important criteria to identify unique populations for conservation purposes. In this study we analyze the genetic population structure of the endangered montane mayfly Ameletus inopinatus in its European range. The species is restricted to unpolluted cold-water streams, and exhibits an insular distribution across highlands of Central Europe and a more continuous distribution across Fennoscandia and Northern Euro-Siberia. We genotyped 389 individuals from 31 populations for eight highly polymorphic microsatellite loci to investigate genetic diversity and population structure within and among European mountain ranges. Genetic diversity of A. inopinatus decreases along an east?Cwest gradient in Central Europe and along a north?Csouth gradient in Fennoscandia, respectively. Centres of exceptionally high genetic diversity are located in the Eastern Alps (Andertal Moor, Austria), the High Tatra, the Beskides, the Sudety Mountains and the Eastern German Highlands. Species distribution modelling for 2080 projects major regional habitat loss, particularly in Central Europe mountain ranges. By relating these range shifts to our population genetic results, we identify conservation units primarily in Eastern Europe, that if preserved would maintain high levels of the present-day genetic diversity and continue to provide long-term suitable habitat under future climate warming scenarios.     

塔克拉玛干沙漠腹地隔离人群线粒体DNA序列多态性分析

对新疆塔克拉玛干沙漠腹地的75名克里雅人线粒体DNA的高可变I区的15996—16401的片段进行了序列分析,在所测定的75个个体中,共检测到68个位点存在变异,界定了71种不同的单倍型。克里雅人群的核昔酸变异度和平均核苷酸差异都介于所报道的东方人群和西方人群之间。根据Neighbor-joining法构建系统发育树,发现中亚的各人群均处于东方人群的亚洲谱系和西方人群的欧洲谱系之间,并且克里雅与新疆维吾尔和境外维吾尔之间的遗传距离最近,表明他们之间有很密切的亲缘关系。     

Diversity among African pygmies

Although dissimilarities in cranial and post-cranial morphology among African pygmies groups have been recognized, comparative studies on skull morphology usually pull all pygmies together assuming that morphological characters are similar among them and different with respect to other populations. The main aim of this study is to compare cranial morphology between African pygmies and non-pygmies populations from Equatorial Africa derived from both the Eastern and the Western regions in order to test if the greatest morphological difference is obtained in the comparison between pygmies and non-pygmies. Thirty three-dimensional (3D) landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies) were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression) and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. Therefore, our findings raise serious doubt about the fact to consider African pygmies as a homogenous group in studies on skull morphology. Differences in cranial morphology among pygmies would suggest differentiation after divergence. Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies.     

Bioethics: an African perspective

In this paper I have attempted to open a window on an African approach to Bioethics — that of the Nso' of the Bamenda Highlands of Kamerun — from the vantage position of someone who has familiarity with both African and Western cultures. Because of its scientific-cum-technological sophistication and its proselytising character, Western culture, as well as Western systems of thought and practice, have greatly affected and influenced other cultures, particularly African culture. But Western culture, systems of thought and practice, have been highly impervious and immune to influences from other cultures, philosophies, systems of thought and practice, even where these might have been salutary and enriching to Western culture and systems. What I have here termed Nso' eco-bio-cummunitarianism clearly indicates a viable alternative world-view within which some of the bioethical perplexities and controversies of today might be more satisfactorily resolved than within a Western framework. I have further attempted to show, by way of example, how within such a world-view, abortion and suicide, for instance, would be disapproved of while euthanasia, in its etymological purity, is approved of.     

How to know about waters? Finnish traditional knowledge related to waters and implications for management reforms

Finnish lakes, rivers, the Baltic and wetlands–our aquatic ecosystems–are surveyed, assessed and studied using natural sciences and ecological data. We argue that this approach is leaving out a key repository of information–the traditional knowledge of waters. By reviewing aspects, qualities and depth of knowledge across Finland from mid-boreal ecosystems in Eastern Finland to large Saimaa lake system to Western Finnish lakes we demonstrate a potentially reformative approach to aquatic assessments. Cultural indicators, baseline data from oral histories, linguistic diversity and behaviour of species on lakes based on traditional knowledge observations have the potential to greatly enhance our understanding of ecosystem health. Of special importance are the spawning locations of fish known through traditional knowledge, but often ignored by science-based assessments.

     

Alternating Ontologies: Exchange and Ritual in Anganen History

In this article I examine the changing social and historical context of exchange and ritual amongst the Anganen of the Southern Highlands Province of Papua New Guinea, a neglected theme in Highland ethnography. I focus primarily on the history of the incorporation of one spirit cult ritual, rimbu, and its relationship to the other major spirit cult, kabit, and just how these two cults inter-relate with two major categories of exchange—the ceremonial pig kill (yasolu) and the more ‘mundane’ forms of exchange associated with such events as marriage and death. It is the structural parallels, differences and interconnections between these two exchange categories and the two ritual types which have guided much of the historical development of local social structure until colonisation. This has resulted in a substantial, though not necessarily stable, integration of ritual and exchange which has been ‘played out’ over the approximately fifteen-year periods between yasolu pig kills. I argue that it is this set of oppositions that provides the structural basis for different potentialities for male capacity. On occasion these may be so graphically distinct that they may be called differing social ontologies, different baselines for being and action. Different aspects of rimbu were adopted from around the turn of the twentieth century until colonisation some 50 years later when both kabit and rimbu were abandoned under mission pressure. However, to talk about the adoption of rimbu and the changes to Anganen social structure which it helped to produce as ‘pre-colonial’ history is misleading to the extent that much of the impetus for change was bound up in the efflorescence of trade caused by the Australian pearling industry in the Torres Strait. I call this period ‘ante-colonial’ in order to highlight the impact of the Australians and the irony that what the Australians indirectly helped create, rimbu as a central feature to Anganen social life, was destroyed with the direct colonial presence and missionisation.     

Microsatellite diversity and structure of Carpathian brown bears (Ursus arctos): consequences of human caused fragmentation

The formerly large, continuous brown bear population of the Carpathians has experienced a radical decrease in population size due to human activities which have resulted in splitting the population into the larger Eastern Carpathian and the smaller Western Carpathian subpopulations. In the Western Carpathians, brown bears came close to extinction at the beginning of 1930s, but thanks to both conservation and management efforts the bear population has begun to recover. In contrast, the Eastern Carpathian subpopulation in Romania has never dropped below 800 individuals, potentially preserving the original amount of genetic variation. In this paper we present results of a genetic study of brown bear subpopulations distributed in the Slovak and Romanian sections of the Carpathians using 13 nuclear microsatellites. The documented level of genetic differentiation between the Western and Eastern Carpathian subpopulations reflects the isolation which lasted almost 100 years. Furthermore, the existence of two, different, genetic clusters within the Western Carpathians despite close geographic proximity indicates that human-caused fragmentation and isolation have resulted in significant genetic divergence. Although the subpopulations display an indication of genetic bottleneck, the level of genetic diversity is within the range commonly observed in different brown bear populations. The results presented here point out the significance of human exploitation to the population structure of this large carnivore species. Future management efforts should be aimed at securing and restoring the connectivity of forested habitats, in order to preserve the genetic variation of the Carpathian brown bear subpopulations and to support the gene flow between them.     

Q型烟粉虱东地中海种群遗传多样性的mtCOI与SSR分析

前期研究表明入侵我国山东的Q型烟粉虱Bemisia tabaci（Genn.）种群来源于西地中海地区而非来源于东地中海地区。为了揭示Q型烟粉虱的入侵遗传机制, 本研究进一步利用线粒体COI（mtCOI）基因与6个具有多态性的微卫星位点（SSR）分析了东地中海Q型烟粉虱（Q1支系与Q2支系）种群的遗传多样性, 并与西地中海种群遗传多样性的前期研究结果进行了比较分析。基于mtCOI基因与微卫星标记分析结果表明, 东地中海种群与西地中海种群一样也具有较高的遗传多样性, 然而两个地区种群存在着遗传异质性。不同入侵性种群遗传结构的比较研究将为进一步解析外来种群的入侵生理生态机制奠定基础。     

Multiple cryptic refugia of forest grass Bromus benekenii in Europe as revealed by ISSR fingerprinting and species distribution modelling

Despite not having been fully recognized, the cryptic northern refugia of temperate forest vegetation in Central and Western Europe are one of the most important in the Holocene history of the vegetation on the subcontinent. We have studied a forest grass Bromus benekenii in 39 populations in Central, Western and Southern Europe with the use of PCR-ISSR fingerprinting. The indices of genetic population diversity, multivariate, and Bayesian analyses, supplemented with species distribution modelling have enabled at least three putative cryptic northern refugial areas to be recognized: in Western Europe—the Central and Rhenish Massifs, in Central Europe—the Bohemia–Moravia region and in the Eastern/Western Carpathians. Central Poland is the regional genetic melting-pot where several migratory routes might have met. Southern Poland had a different postglacial history and was under the influence of an Eastern/Western Carpathian cryptic refugium. More forest species should be checked in a west–east gradient in Europe to corroborate the hypothesis on the Western European glacial refugia.