Roe deer on ice: Selection despite limited effective population size through the Pleistocene

Roe deer (Capreolus spp.) are a little odd. They are one of only a few placental mammals—and the only genus among even‐toed ungulates—capable of putting embryonic development “on ice”, also known as embryonic diapause (Figure 1). It would seem such an unusual trait is probably the product of natural selection, but a big question is, how does selection for important traits, such as diapause, interact with the historical demography of a species? In a ‘From the Cover’ article in this issue of Molecular Ecology, de Jong et al. (2020) demonstrate that selection is acting on genes associated with reproductive biology in roe deer, despite heightened genetic drift due to reduced effective population size through the Pleistocene.     

Arcobacter ellisii sp. nov., isolated from mussels

As part of a study carried out for detecting Arcobacter spp. in shellfish, three mussel isolates that were Gram-negative slightly curved rods, non-spore forming, showed a new 16S rDNA-RFLP pattern with a specific identification method for the species of this genus. Sequences of the 16S rRNA gene and those of the housekeeping genes rpoB, gyrB and hsp60 provided evidence that these mussel strains belonged to an unknown genetic lineage within the genus Arcobacter. The similarity between the 16S rRNA gene sequence of the representative strain (F79-6^T) and type strains of the other Arcobacter species ranged between 94.1% with A. halophilus and 99.1% with the recently proposed species A. defluvii (CECT 7697^T). DDH results between strain F79-6^T and the type strain of the latter species were below 70% (53 ± 3.0%). Phenotypic characteristics together with MALDITOF mass spectra differentiated the new mussel strains from all other Arcobacter species. All the results indicate that these strains represent a new species, for which the name Arcobacter ellisii sp. nov. with the type strain F79-6^T (=CECT 7837^T = LMG 26155^T) is proposed.     

Determining patterns of genetic diversity and post‐glacial recolonization of western Canada in the Iowa golden saxifrage,Chrysosplenium iowense (Saxifragaceae), using inter‐simple sequence repeats

Chrysosplenium iowense Rydb. (Saxifragaceae) is a southern Canadian boreal forest species with a small number of disjunct populations occurring in the Driftless Area of northeastern Iowa and southeastern Minnesota. This disjunction is attributed to the actions of glacial movement and climate change during the Pleistocene. Populations within each of these distributions may have been isolated for 115 000 years or more and, although levels of genetic divergence between these regions may be significant, there is no morphological or cytological variation associated with this geographic break. We employed inter‐simple sequence repeat (ISSR) markers to determine patterns of genetic diversity within 12 populations (six Canadian; six Iowan) of C. iowense and elucidate the routes of post‐glacial recolonization for the species. Despite finding relatively high levels of genetic divergence (θ^II = 0.383, θ^II = 0.299) between Driftless Area and Canadian populations, there is no conclusive evidence of a speciation event within C. iowense. Analyses show moderate levels of genetic diversity within the species (H_T = 0.188), the majority of which is partitioned among individuals within populations (68.18%), which were similar across the northern (H_T = 0.234, H_T = 0.28) and southern (H_T = 0.189) ranges. Finally, the patterns of genetic diversity within C. iowense suggest that the Canadian range was established by migrants originating in now extinct refugial populations that existed outside the Driftless Area. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 815–823.     

The evolution of mammalian body temperature: the Cenozoic supraendothermic pulses

In this study, I investigated the source(s) of variation in the body temperatures of mammals. I also attempted to reconstruct ancestral normothermic rest-phase body temperature states using a maximum parsimony approach. Body temperature at the familial level is not correlated with body mass. For small mammals, except the Macroscelidae, previously identified correlates, such as climate adaptation and zoogeography explained some, but not all, T _b apomorphies. At the species level in large cursorial mammals, there was a significant correlation between body temperature and the ratio between metatarsal length and femur length, the proxy for stride length and cursoriality. With the exception of two primate families, all supraendothermic (T _b > 37.9°C) mammals are cursorial, including Artiodactyla, Lagomorpha, some large Rodentia, and Carnivora. The ruminant supraendothermic cursorial pulse is putatively associated with global cooling and vegetation changes following the Paleocene–Eocene Thermal Maximum. Reconstructed ancestral body temperatures were highly unrealistic deep within the mammalian phylogeny because of the lack of fossil T _b data that effectively creates ghost lineages. However, it is anticipated that the method of estimating body temperature from the abundance of ¹³C–¹⁸O bonds in the carbonate component of tooth bioapatite in both extant and extinct animals may be a very promising tool for estimating the T _b of extinct mammals. Fossil T _b data are essential for discerning derived T _b reversals from ancestral states, and verifying the dates of supraendothermic pulses.     

Shallow genetic divergence and species delineations in the endemic Labeobarbus species flock of Lake Tana,Ethiopia

To assess whether the species distinctions of Lake Tana's Labeobarbus spp. are supported by genetic information, microsatellite markers were used. A total of 376 Labeobarbus spp., belonging to 24 populations of 11 species from three regions of the lake (north, south and east), were sampled. Eight microsatellite markers were analysed. In general, differences between conspecific populations were smaller than differences between populations of different species. For six species, conspecific populations from different regions in the lake were consistently more similar than populations of other species from the same region. For four species this was not the case, while for one species two populations were similar, but different from the third population. River‐spawning species appeared to be more distinct than presumed lake spawners. On the species level, there was a significant correlation between genetic and morphological differentiation, especially in morphological aspects associated with ecological functioning. This suggests that genetic differentiation arose together with adaptive radiation, although the overall genetic differentiation among the Lake Tana Labeobarbus spp. is small.     

Impacts of ungulates on the demography and diversity of small mammals in central Kenya

The impacts of ungulates on small mammals in an East African savanna habitat were investigated by monitoring the population and community responses of small mammals on replicated 4-ha plots from which ungulates had been excluded. The dominant small mammal in this habitat is the pouched mouse, Saccostomusmearnsi, a medium-sized murid rodent. Eight other small mammal species, including Arvicanthis sp., Mus sp., Mastomys sp., Dendromus sp., Crocidura sp., and, rarely, Tatera sp., Aethomys sp., and Acomys sp., were also captured. The dominant ungulates are elephant (Loxodonta africana), giraffe (Giraffa camelopardalis), Grevy's and common zebra (Equus grevyi and E. burchelli), buffalo (Syncerus cafer), eland (Taurotragus oryx), Grant's gazelle (Gazella granti), and domestic cattle. Within 1 year, S. mearnsi populations had responded dramatically to the exclusion of large mammals by a two-fold increase in density, a difference that was maintained through pronounced seasonal fluctuations in the second year. Though individual pouched mice showed no significant differences in their use of space with and without ungulates, male S. mearnsi maintained significantly higher body weights in the absence of ungulates, indicating that habitat quality had increased. One other species, Mastomys sp., also increased in the absence of ungulates. Overall, the small mammal community maintained relatively constant species diversity on the plots to which ungulates did not have access. On the plots to which ungulates did have access, on the other hand, there was a rapid 75% decrease in diversity in the control plots during one trapping session. Ungulates are most likely affecting small mammals through their effects on food quality, since there were no detectable differences in their exposure to predators, as determined by vegetative cover, in the absence of ungulates. These results demonstrate that ungulates can have strong and rapid impacts on small mammal abundance and diversity in East African savannas, an interaction which has not previously been given serious consideration. Received: 28 December 1997 / Accepted: 11 May 1998     

DISTRIBUTION OF KRANZ SYNDROME AMONG ASTERACEAE

A broad survey of the Asteraceae, involving visual characters, was undertaken to ascertain the occurrence of possible Kranz-type (C₄) plants. One hundred and seven taxa representing 51 genera were examined by mass spectrometry for their ¹³C/¹²C ratios in dried leaf tissue. Species possessing the high ¹³C/¹²C ratio typical of the Kranz syndrome were found in genera belonging to the following tribes: Heliantheae (subtribe Coreopsideae)—Chrysanthellum (4 spp.), Eryngiophyllum (1 sp.), Glossocardia (1 sp.), Glossogyne (1 sp.), Isostigma (5 spp.); Tageteae—Pectis (21 spp.); and Helenieae—Flaveria (4 spp.). The only genus to possess both C₃ and C₄ species was Flaveria in which all but four species appear to possess a C₃-type metabolism. When appropriate, the phyletic input of these data is discussed.     

Resting metabolic rate and lung function in fasted and fed rough-toothed dolphins,Steno bredanensis

We measured resting metabolic rate (RMR), tidal volume (V_T), breathing frequency (f_R), respiratory flow, and end-expired gases in rough-toothed dolphins (Steno bredanensis) housed in managed care after an overnight fast and 1–2 hr following a meal. The measured average (± standard deviation) V_T (4.0 ± 1.3 L) and f_R (1.9 ± 1.0 breaths/min) were higher and lower, respectively, as compared with estimated values from both terrestrial and aquatic mammals, and the average V_T was 43% of the estimated total lung capacity. The end-expired gas levels suggested that this species keep alveolar O₂ (10.6% or 80 mmHg) and CO₂ (7.6% or 57 mmHg), and likely arterial gas tensions, low and high, respectively, to maximize efficiency of gas exchange. We show that following an overnight fast, the RMR (566 ± 158 ml O₂/min) was 1.8 times the estimated value predicted by Kleiber for terrestrial mammals of the same size. We also show that between 1 and 2 hr after ingestion of a meal, the metabolic rate increases an average of 29% (709 ± 126 ml O₂/min). Both body mass (M_b) and f_R significantly altered the measured RMR and we propose that both these variables should be measured when estimating energy use in cetaceans.     

Effects of copper on species composition of periphyton in a Sierra Nevada, California, stream

SUMMARY. 1. Changes in species composition of the periphyton of an oligotrophic. Sierra Nevada stream continuously dosed for 1 year at three concentrations of copper (2.5, 5 and 10 μg 1^?1 Cu_T; approximately 12, 25 and 50 ng 1^?1 Cu²⁺) were determined. 2. The numerically most abundant taxa were Bacillariophyceae (Achnanthes minutissima, Cocconeis placentula, Cymbella microcephala, C. sinuata, Fragilaria conslruens, F. crotonensis. Navicula spp., Synedra acus and S. rumpens), and the Cyanophyta Lyngbya spp., a co-dominant during spring and summer. 3. Population densities of Lyngbya spp. were markedly reduced at all test concentrations of copper. Population densities of the principal Chlorophyta (Spirogyra spp. and Cladophora spp.) and the diatom Amphipleura pellucida were reduced at 5 μg 1^?1 CU_T. Of the twenty-two most abundant taxa, sixteen were reduced in abundance by continuous exposure to 10 μg 1^?1 Cu_T. 4. There was no commensurate reduction in standing crop (total number of individuals of all taxa). Achnanthes minutissima, a co-dominant in the control, was the primary replacement species. Other taxa that were more abundant at 5 μg1^?1 Cu_T than in the control were Ceratoneis arcus, Cocconeis placentula, Navicula spp. and Synedra rumpens. Only A. minutissima and Calothrix spp. were more abundant at 10 μg 1^?1 than in the control. 5. Three resemblance measures (Canberra metric, Bray-Curtis and Dice) and diversity (Brillouin's) were evaluated for detecting differences in species composition among experimental stream sections. The Canberra metric, an index sensitive to proportional rather than absolute differences, was the most informative of these indices.     

Phylogenetic aspects of Cetacean origins: A morphological perspective

The evolutionary steps leading up to the origin of cetaceans involved pervasive changes in the masticatory apparatus, the ear, and limb morphology. These changes bear heavily on the phylogenetic relationships of Cetacea, and are investigated here on the basis of two of its earliest members:Pakicetus andAmbulocetus. A phylogenetic analysis of cetaceans, five groups of mesonychians, and five other groups of ungulates indicates thatPakicetus is the sister group to all other cetaceans, and that Cete (mesonychians and Cetacea) is a monophyletic group.     

<Emphasis Type="Italic">Aquimarina salinaria</Emphasis> sp. nov., a novel algicidal bacterium isolated from a saltpan

A bacterial strain designated antisso-27^T, previously isolated from saltpan in Taiwan while screening for bacteria for algicidal activity, was characterized using the polyphasic taxonomic approach. Strain antisso-27^T was Gram-negative, aerobic, brownish yellow colored, rod-shaped, non-flagellated and non-gliding. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain antisso-27^T belonged to the genus Aquimarina within the family Flavobacteriaceae with relatively low sequence similarities of 94.0–96.6% to other valid Aquimarina spp. It contained iso-C_17:0 3-OH, iso-C_15:0, iso-C_16:0, iso-C_15:1 and iso-C_15:0 3-OH as the main fatty acids and contained a menaquinone with six isoprene units (MK-6) as the major isoprenoid quinone. Major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, an uncharacterized aminolipid and five uncharacterized phospholipids. Strain antisso-27^T employed direct mode of algicidal lysis to Chlorella vulgaris strain 211-31; nevertheless, it released an algicidal substance against M. aeruginosa strain MTY01. This is the first study that the Aquimarina species possesses both direct and indirect algicidal activities. On the basis of the phylogenetic and phenotypic data, strain antisso-27^T should be classified as representing a novel species, for which the name A. salinaria sp. nov. is proposed. The type strain is A. salinaria antisso-27^T (= BCRC 80080^T = LMG 25375^T).     

A biogeographical regionalization of Angolan mammals

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WHO ARE THE WHALES?

ABSTRACT

Whales, dolphins and porpoises, 80 species of entirely aquatic mammals, constitute the order Cetacea. In the early Eocene, about 55 to 60 million years ago according to paleontologists, distant ancestors of modern cetaceans left land for aquatic life. Cetaceans are diverse; average adult size of cetacean species varies by 1000 to 2000 times. Small and large species occupy all oceans from the equator to the polar seas, some forms inhabit rivers and four species live only in fresh water.

Cetaceans are born in water and spend their entire lives in the aquatic medium. There is a great gap in knowledge about hearing in most cetacean species and especially about how noise and high-intensity sound may affect all cetaceans and other mammals underwater. Studies of temporary threshold shift (TTS) and occupational noise exposure in human divers suggest a cautious approach to cetacean noise exposure until data on cetacean TTS can give us some idea of the dynamic range of cetacean ears.     

Kibdelosporangium phytohabitans sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. containing 1-aminocyclopropane-1-carboxylic acid deaminase

A novel actinomycete, designated strain KLBMP 1111^T, was isolated from the root of the oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China. Strain KLBMP 1111^T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Kibdelosporangium, with the highest similarity to Kibdelosporangium aridum subsp. aridum DSM 43828^T (98.8%), K. aridum subsp. largum DSM 44150^T (98.1%) and Kibdelosporangium philippinense DSM 44226^T (98.1%). The organism produced sporangium-like structures, the typical morphological characteristic of the genus Kibdelosporangium. The chemotaxonomic properties of this strain were also consistent with those of the genus Kibdelosporangium: the peptidoglycan contained meso-diaminopimelic acid; the predominant menaquinone was MK-9(H₄); phospholipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol and an unknown phospholipid; iso-C_16:0, C_16:0, anteiso-C_15:0 and iso-C_15:0 as the predominant cellular fatty acids and the G+C content was 67.2 mol%. DNA–DNA hybridization values between strain KLBMP 1111^T and the three Kibdelosporangium species were less than 50%. This strain had the ability to produce a siderophore, utilized 1-aminocyclopropane-1-carboxylic acid (ACC) as sole source of nitrogen and possessed ACC deaminase enzyme. Based on genotypic and phenotypic data, strain KLBMP 1111^T represents a novel species in the genus Kibdelosporangium. We propose the name Kibdelosporangium phytohabitans sp. nov. for this species. The type strain is the strain KLBMP 1111^T (=KCTC 19775^T = CCTCC AA 2010001^T).     

Paenibacillus tylopili sp.nov., a chitinolytic bacterium isolated from the mycorhizosphere of Tylopilus felleus

Two chitinolytic bacterial strains (designated MK2^T and V7) were isolated from the mycorhizosphere of the fungus Tylopilus felleus. The strains were facultatively anaerobic G⁺ endospore formers. Physiological analysis and 16S rRNA gene PCR-RFLP assays revealed nearly identical profiles for both strains, demonstrating their relationship at the species level. Sequences specific for the genus Paenibacillus were found within the 16S rRNA gene sequence of the strain MK2^T. The 16S rRNA gene sequence showed the highest similarity to the sequences of Paenibacillus amylolyticus, P. pabuli and P. xylanilyticus. DNA-DNA relatedness of the strain with the type strain of P. amylolyticus was 4.95 %, of P. pabuli 38.0 %, and of P. xylanilyticus 46.3 %, indicating no relatedness between MK2^T and any of them at the species level. The most abundant fatty acids in strains MK2^T and V7 were anteiso-C_15:0, iso-C_16:0, iso-C_15:0 and n-C_16:0. DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses, and phylogenetic data based on 16S rRNA gene sequencing made it possible to describe both strains as the novel species of the genus Paenibacillus, for which the name Paenibacillus tylopili is proposed, the type strain being MK2^T (DSM 18927^T, LMG 23975^T).     

Nitratireductor lucknowense sp. nov., a novel bacterium isolated from a pesticide contaminated soil

A straw-yellow pigmented bacterium, strain IITR-21^T was isolated from a pesticide contaminated site and characterized by using a polyphasic taxonomic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genus Nitratireductor. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain IITR-21^T belongs to the genus Nitratireductor and was moderately related to Nitratireductor indicus C115^T (97.7%) and Nitratireductor pacificus pht-3B^T (97.4%), whereas sequence similarity value with the other species including the type species of the genus Nitratireductor, Nitratireductor aquibiodomus showed less than 97.0% similarity. However, the DNA–DNA relatedness values between strain IITR-21^T and the moderately related taxa N. indicus (59.1%) and N. pacificus (40.4%) were well below the 70% threshold value recommended for the delineation of bacterial species. The G+C content of the DNA was 62.4 mol%. Based on physiological, biochemical tests and genotypic differences between the strain IITR-21^T and the other two validly published species of the genus Nitratireductor, it is proposed that the strain be classified as a new species of Nitratireductor as Nitratireductor lucknowense sp. nov. The type strain is IITR-21^T (=MTCC 8354^T = DSM 24322^T).     

<Emphasis Type="Italic">Protungulatum</Emphasis>, Confirmed Cretaceous Occurrence of an Otherwise Paleocene Eutherian (Placental?) Mammal

Neither pre-Cenozoic crown eutherian mammals (placentals) nor archaic ungulates (“condylarths”) are known with certainty based on the fossil record. Herein we report a new species of the Paleocene archaic ungulate (“condylarth”) Protungulatum from undisputed Late Cretaceous aged rocks in Montana USA based on an isolated last upper premolar, indicating rare representatives of these common early Tertiary mammals appeared in North America a minimum of 300 k  years before the extinction of non-avian dinosaurs. The other 1200 mammal specimens from the locality are characteristic Late Cretaceous taxa. This discovery overturns the current hypothesis that archaic ungulates did not appear in North America until after the Cretaceous/Tertiary (K/T) boundary and also suggests that other reports of North American Late Cretaceous archaic ungulates may be correct. Recent studies, including ours, cannot determine whether Protungulatum does or does not belong to the crown clade Placentalia.     

<Emphasis Type="Italic">Luteimonas aestuarii</Emphasis> sp. nov., isolated from tidal flat sediment

A novel bacterium B9^T was isolated from tidal flat sediment. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow and the cells are Gram-negative, rod-shaped, and do not require NaCl for growth. The 16S rRNA gene sequence similarity indicated that strain B9^T is associated with the genus Lysobacter (≤ 97.2%), Xanthomonas (≤ 96.8%), Pseudomonas (≤ 96.7%), and Luteimonas (≤ 96.0%). However, within the phylogenetic tree, this novel strain shares a branching point with the species Luteimonas composti CC-YY255^T (96.0%). The DNA-DNA hybridization experiments showed a DNA-DNA homology of 23.0% between strain B9^T and Luteimonas mephitis B1953/27.1^T. The G+C content of genomic DNA of the type strain is 64.7 mol% (SD, 1.1). The predominant fatty acids are iso-C_11:0, iso-C_15:0, iso-C_16:0, iso-C_17:0, iso-C_17:0 ω9c, and iso-C_11:0 3-OH. Combined analysis of the 16S rRNA gene sequences, fatty acid profile, and results from physiological and biochemical tests indicated that there is genotypic and phenotypic differentiation of the isolate from other Luteimonas species. For these reasons, strain B9^T was proposed as a novel species, named Luteimonas aestuarii. The type strain of the new species is B9^T (= KCTC 22048^T, DSM 19680^T).     

Branchiibius cervicis sp. nov., a novel species isolated from patients with atopic dermatitis

Novel actinobacterial strains, PAGU 1247^T, PAGU 1251 and PAGU 1252, were isolated from the skin of atopic dermatitis patients and were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were located within the family Dermacoccaceae. The most closely related species of PAGU 1247^T in phylogenetic terms was Branchiibius hedensis Mer 29717^T, with 16S rRNA gene sequence similarity of 99.6%, although the DNA–DNA relatedness value was less than 43.9%. Some biochemical traits, such as lipase (C14) and α-galactosidase activity, could distinguish these isolates from B. hedensis. Strain PAGU 1247^T contained iso-C_16:0 and brC_18:0 as the major fatty acids. The quinone system consisted of menaquinone MK-8(H₆ and H₄). The G + C content of the genomic DNA was 67.6 mol%. On the basis of its phenotypic properties and genetic distinctiveness, strains PAGU 1247^T, PAGU 1251 and PAGU 1252 represents a novel species of the genus Branchiibius, for which the name Branchiibius cervicis sp. nov. is proposed. The type strain is PAGU 1247^T (=NBRC 106593^T = DSM 24166^T).     

Demography, and genetic and morphological variability of the endangered Sophronitis sincorana (Orchidaceae) in the Chapada Diamantina, Brazil

We carried out a demographic study and evaluated the genetic and morphological variability in five populations of the endangered Sophronitis sincorana (Orchidaceae) endemic to Northeastern Brazil, based on allozyme and morphometric analyses. Plant density was approximately 0.5 plants/m², and the projected total number of plants was approximately 50,000 individuals. However, fruit set and recruitment of individuals are rare. The genetic variability was very high in all populations (P = 100, A = 3.0−3.5, H _e = 0.33−0.48), and all populations presented similar values of morphological variability. Low genetic and morphological structuring were found in the species (F _ST = 0.053, A_MRPP = 0.018). The elevated coefficient of endogamy encountered in populations of S. sincorana indicates the occurrence of structuring within the populations. The lack of correlation between morphological and genetic variation in this species indicates that none of the markers examined should be used separately for either conservation purposes.