Comparative proteomics reveals evidence for evolutionary diversification of rodent seminal fluid and its functional significance in sperm competition

During insemination, males of internally fertilizing speciestransfer a complex array of seminal fluid proteins to the femalereproductive tract. These proteins can have profound effectson female reproductive physiology and behavior and are thoughtto mediate postcopulatory sexual selection and intersexual conflict.Such selection may cause seminal fluid to evolve rapidly, withpotentially important consequences for speciation. Here we investigatethe evolution of seminal fluid proteins in a major mammalianradiation, the muroid rodents, by quantifying diversity in seminalfluid proteome composition for the first time across a broadrange of closely related species. Using comparative proteomicstechniques to identify and cross-match proteins, we demonstratethat rodent seminal fluid is highly diverse at the level ofboth proteomes and individual proteins. The striking interspecificheterogeneity in seminal fluid composition revealed by our surveyfar exceeds that seen in a second proteome of comparable complexity,skeletal muscle, indicating that the complement of proteinsexpressed in seminal fluid may be subject to rapid diversification.We further show that orthologous seminal fluid proteins exhibitsubstantial interspecific variation in molecular mass. Becausethis variation cannot be attributed to differential glycosylationor radical differences in termination sites, it is stronglysuggestive of rapid amino acid divergence. Sperm competitionis implicated in generating such divergence for at least onemajor seminal fluid protein in our study, SVS II, which is responsiblefor copulatory plug formation via transglutaminase-catalyzedcross-linking after insemination. We show that the molecularmass of SVS II is positively correlated with relative testissize across species, which could be explained by selection foran increased number of cross-linking sites involved in the formationof the copulatory plug under sperm competition.     

中国兽类一新纪录白尾高山䶄及西藏、湖北和四川兽类各一省级新纪录

在最近几年开展的小型兽类调查和研究中,通过形态学和分子鉴定的方法,证实在新疆发现的白尾高山䶄（Alticola albicauda True, 1894）是中国新纪录。该种尾全白色,末端有白色毛束;身体背部淡红褐色,腹部纯白。在基于Cyt b构建的系统树中和GenBank中的白尾高山䶄聚在一起,并与银色高山䶄（Alticola argentatus Severtzov,1879）形成姊妹群,两者间遗传距离为5%;在西藏发现小毛足鼠（Phodopus roborovskii Satunin,1902）,其特征和我国其他区域分布的小毛足鼠一致,两者之间Cyt b基因遗传距离（K2P）为0.6%,是西藏新纪录;在四川发现丽江绒鼠（Eothenomys fidelis Hinton, 1923）,牙齿特征,尾长和体长之比和地模标本基本一致,但个体较小,在基于Cyt b构建的系统发育树显示,四川标本为独立分支,表明形态和分子上均存在一定的分化,但和地模标本的遗传 距离只有1.1%,应为同一种,为四川省新纪录;在湖北发现循化鼠兔（Ochotona xunhuaensis Sou and Feng, 1984）,有异耳屏,头骨较扁平,符合循化鼠兔的鉴定特征,与模式产地的循化鼠兔Cyt b基因的遗传距离为1.9%,为湖北新纪录。     

Future hotspots of terrestrial mammal loss

Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world.     

Ancient introductions of mammals in the Mediterranean Basin and their implications for conservation

• 1 The importance of taxonomy to the determination of conservation priorities and actions is widely accepted. It should be not surprising therefore that the taxonomic treatment of mammal species that have been subject to human actions in antiquity may well influence the contemporary assessment of conservation priorities at various levels.
• 2 As a result of early extinctions caused by humans and protohistoric and historic introductions, we suggest that the Mediterranean Basin and its islands are particularly prone to misdirection of efforts towards biodiversity conservation.
• 3 The two main risks associated with the failure to use an evolutionary and palaeoecological approach to conservation efforts are (i) an underestimation of the conservation importance of distinctive continental taxa vs. the apparent endemicity of island taxa; and (ii) a serious risk for native and endemic island species when anthropochorous mammals, especially ungulates, misguidedly become the focus of conservation actions, particularly inside protected areas.
• 4 Urgent measures, including refinement of mammal taxonomy, the exclusion of known anthropochorous taxa from conservation lists and implementation of protective legislation, are necessary to maintain the uniqueness and richness of the Mediterranean biodiversity hotspot.

     

A Holocene sequence of vegetation change at Lake Eteza, coastal KwaZulu-Natal, South Africa

Palynological and sedimentological data from a core extracted from Lake Eteza shed new light on the Holocene vegetation and climate history in KwaZulu-Natal and can be linked to regional and global climate change. A 2072 cm core with nineteen radiocarbon dates and chronological extrapolation to the bottom of the sequence suggests that sedimentation started ca. 10 200 cal yrs BP. Between ca. 10 200 and 6800 cal yrs BP pollen indicators point to a change from intermediately humid conditions to comparatively drier grassy environments. This is in good agreement with Sea Surface Temperature (SST) fluctuations from a core in the Mozambique Channel which influence precipitation in coastal KwaZulu-Natal, and the beginning of the Holocene Thermal Maximum ca. 10 500 cal yrs BP. The lower section of the core corresponds to gradually increasing Holocene sea levels along the coast and development of freshwater or estuarine conditions at Lake Eteza. The middle Holocene (ca. 6800-3600 cal yrs BP), when the sea level reached its highest stand and SST peak, indicate humid climatic conditions that favoured an increase of forest trees, e.g. Podocarpus, and undergrowth plants like Issoglossa. As a consequence of higher precipitation and increase of the water table, conditions were favourable for the spread of mangrove, swamp and possibly riverine forest. During the late Holocene after ca. 3600 cal yrs BP a decrease of Podocarpus and other trees as well as an increase of Chenopodiaceae/Amaranthaceae, grasses and Phoenix coincide with a return to lower sea levels and drier conditions. The decrease of all trees including Phoenix at ca. 700 cal yrs BP, accompanied by rapid sedimentation rates, possibly reflect forest clearing and upland erosion induced by activities of Iron Age settlers. A dry period at the globally recognized onset of the Little Ice Age might have contributed to these changes. Late Iron Age settlers have probably already introduced Zea mays, which was detected in the profile since ca. 210 BP. The appearance of neophytes like Pinus, Casuarina and pollen of Ambrosia-type in the youngest sediments indicates increased disturbance of European settlements and land use since ca. 100 cal yrs BP.     

Size variation facilitates population divergence but does not explain it all: an example study from a widespread African monkey

Subspecific variation is widespread in vertebrates. Within Africa, several mammals have extensive geographic distributions with attendant morphological, ecological, and behavioural variations, which are often used to demarcate subspecies. In the present study, we use a primate species, the vervet monkey, Cercopithecus aethiops, as a case study for intraspecific divergence in widespread mammals, assessed through hard tissue morphology. We examine intraspecific differences in size, shape, and non‐allometric shape from a taxonomic perspective, and discuss the macroevolutionary implications of findings from microevolutionary analyses of geographic variation. A geometric morphometric approach was used, employing 86 three‐dimensional landmarks of almost 300 provenanced crania. Many of the taxonomic differences in skull morphology between vervet populations appear to be related to geographic proximity, with subspecies at opposite extremes of a west‐to‐east axis showing greatest divergence, and populations from central and south Africa being somewhat intermediate. The classification rate from discriminant analyses was lower than that observed in other African primate radiations, including guenons as a whole and red colobus. Nonetheless, taxonomic differences in shape were significant and not simply related to either geography or size. Thus, although shifts in size may be an important first step in adaptation and diversification, with size responding more quickly than shape to environmental change, the six vervet taxa currently recognized (either as species or subspecies) are not simply allometrically scaled versions of one another and are probably best viewed as subspecies. Holding allometry constant when examining inter‐population differences in shape may thus help to reveal the early stages of evolutionary divergence. The vervet case study presented here hence has relevance for future studies examining intraspecific differentiation in other large mammals, particularly through the methods used to identify small but biologically meaningful divergence, with attendant implications for conservation planning. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 823–843.     

DNA polymerase X of African swine fever virus: insertion fidelity on gapped DNA substrates and AP lyase activity support a role in base excision repair of viral DNA

DNA polymerase X (pol X) from African swine fever virus (ASFV) is the smallest naturally ocurring DNA-directed DNA polymerase (174 amino acid residues) described so far. Previous biochemical analysis has shown that ASFV pol X is a highly distributive, monomeric enzyme, lacking a proofreading 3'-5' exonuclease. Also, ASFV pol X binds intermediates of the single-nucleotide base excision repair (BER) process, and is able to efficiently repair single-nucleotide gapped DNA. In this work, we perform an extensive kinetic analysis of single correct and incorrect nucleotide insertions by ASFV pol X using different DNA substrates: (i) a primer/template DNA; (ii) a 1nt gapped DNA; (iii) a 5'-phosphorylated 1nt gapped DNA. The results obtained indicate that ASFV pol X exhibits a general preference for insertion of purine deoxynucleotides, especially dGTP opposite template C. Moreover, ASFV pol X shows higher catalytic efficiencies when filling in gapped substrates, which are increased when a phosphate group is present at the 5'-margin of the gap. Interestingly, ASFV pol X misinserts nucleotides with frequencies from 10(-4) to 10(-5), and the insertion fidelity varies depending on the substrate, being more faithful on a phosphorylated 1nt gapped substrate. We have analyzed the capacity of ASFV pol X to act on intermediates of BER repair. Although no lyase activity could be detected on preincised 5'-deoxyribose phosphate termini, ASFV pol X has lyase activity on unincised abasic sites. Altogether, the results support a role for ASFV pol X in reparative BER of damaged viral DNA during ASFV infection.     

Patterns of bird migration phenology in South Africa suggest northern hemisphere climate as the most consistent driver of change

Current knowledge of phenological shifts in Palearctic bird migration is largely based on data collected on migrants at their breeding grounds; little is known about the phenology of these birds at their nonbreeding grounds, and even less about that of intra‐African migrants. Because climate change patterns are not uniform across the globe, we can expect regional disparities in bird phenological responses. It is also likely that they vary across species, as species show differences in the strength of affinities they have with particular habitats and environments. Here, we examine the arrival and departure of nine Palearctic and seven intra‐African migratory species in the central Highveld of South Africa, where the former spend their nonbreeding season and the latter their breeding season. Using novel analytical methods based on bird atlas data, we show phenological shifts in migration of five species – red‐backed shrike, spotted flycatcher, common sandpiper, white‐winged tern (Palearctic migrants), and diederik cuckoo (intra‐African migrant) – between two atlas periods: 1987–1991 and 2007–2012. During this time period, Palearctic migrants advanced their departure from their South African nonbreeding grounds. This trend was mainly driven by waterbirds. No consistent changes were observed for intra‐African migrants. Our results suggest that the most consistent drivers of migration phenological shifts act in the northern hemisphere, probably at the breeding grounds.     

Growth performance and feed conversion of Ruspolia differens on plant-based by-product diets

The use of food industry by-products in insect feeds has gained increasing attention recently. However, the understanding of how well the economically valuable edible insect Ruspolia differens (Serville) (Orthoptera: Tettigoniidae) can grow and develop with plant-based by-product feeds is currently lacking. It is important to determine the nutritional requirements, especially protein demand, of this species before developing artificial feeds for mass-rearing. We reared R. differens with four control diets and 12 plant-based by-product diets in which the major protein source came from food industry by-products, including potato-protein, barley mash, barley feed, turnip rape, a mix of broad bean and pea, and a mix of potato, carrot, and apple. We asked whether the performance (development time, survival, and weight), feed conversion, and fatty acid composition and content differed among diet treatments. Furthermore, the 12 experimental by-product diets were designed to reach six protein levels. We found that R. differens can be reared with various by-product diets, but development time, survival, and weight differed among diets. Barley feed, barley mash, and potato protein diets seem to be good options for rearing, and potato glycoalkaloids do not affect the performance of R. differens. Individuals fed on the various by-product diets also differed in their fatty acid composition and content. Increasing protein levels in diet up to 17% enhanced growth, development time, and survival, but no further enhancements were seen when fed diets with protein levels higher than this. The high protein levels decreased feed conversion rate. Our results can be valuable for designing feeds for insect mass-rearing technology. The use of food industry by-products in the diets for R. differens could increase the re-use of local resources and enhance circular economy.