Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts

Glycine subgenus Glycine , the sister group to the cultivated soybean and its progenitor, have received considerable study over several decades. The combination of biosystematic data and an extensive germplasm collection has provided a strong foundation for molecular systematic studies in the group, including those on allopolyploids. These studies have shown that the various polyploid taxa known from the subgenus are all part of a single large allopolyploid complex, linked by shared diploid genomes. Many elements of the complex have arisen recently, and most show evidence of recurrent origins. However, there are also many dissimilarities among even closely related polyploids. Polyploids differ from one another in such ways as number of origins, amount of allelic diversity harboured at different loci, bidirectional vs. unidirectional origins, retention of ribosomal gene homoeologues, success as measured by geographical range and abundance, and patterns of gene expression.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 583–597.     

A Late Devonian plant assemblage from the Avon Gorge, west England: taxonomic, phylogenetic and stratigraphic implications

Plant fossils from the Avon Gorge originally identified as Rhacophyton sp. have been subjected to a detailed morphological study incorporating examination of both previously known material and new specimens. A single taxon, Chlidanophylon dublinensis, dominates the assemblage accounting for over 90% of the fossils encountered. Other plant organs identified include dispersed acupulate preovules and five less frequently occurring organs of which four are of unknown affinities; the leaf genus Platyphyllum, Alicomopleris sp., two kinds of novel and frequendy dichotomizing branching structures and the spermatophyte synangium Telangiopsis. Possible whole plant relationships between the components of the fossil assemblage are discussed and the stratigraphic, systematic and evolutionary position of the component taxa are considered.     

Condition,Survival, and Cause-Specific Mortality of Adult Female Mule Deer in North-Central New Mexico

Abstract: From December 2001 to December 2004 we monitored 30–44 adult female mule deer (Odocoileus hemionus) annually to assess the factors affecting survival and cause-specific mortality. We found adult female survival of 0.63 (SE = 0.08), 0.90 (SE = 0.05), and 0.91 (SE = 0.04), 2002–2004, respectively. Starvation was the most common cause of mortality, accounting for 11/23 mortalities. Mean ingesta-free body fat (IFBF) levels of adult females in December were low (6–9%), despite few (0–13%) lactating adult females, indicative of extremely nutritionally deficient summer—autumn ranges throughout the study site. A priori levels of IFBF and rump body condition scores (rBCS) were higher in deer that survived the following year regardless of cause of mortality. Logistical analysis indicated that models containing individual body fat, rBCS, mean population body fat, winter precipitation, precipitation during mid- to late gestation, and total annual precipitation were related (x² ≥ 9.1; P ≤ 0.003) to deer survival, with individual IFBF (β =-0.47 [SE = 0.21]; odds ratio = 0.63 [0.42-0.94]) and population mean IFBF (β = -1.94 [SE = 0.68]; odds ratio = 0.14 [0.04-0.54]) the best predictors; with either variable, probability of dying decreased as fat levels increased. Fawn production was low (2–29 fawns/100 ad F) and, combined with adult survival, resulted in estimated population rates of increase of -35%, -5%, and +6% for 2002–2004, respectively. Deer survival and population performance were limited in north-central New Mexico, USA, due to poor condition of deer, likely a result of limited food resulting from both drought and long-term changes in plant communities. Precipitation during mid- to late gestation was also important for adult female survival in north-central New Mexico.     

Selective predation by Lestes (Odoiiata, Lestidae) on littoral microcrustacea

• 1 Two experimental approaches were used to examine the predation risk of six littoral cladoceran and ostracod species to two size classes of the damselfly Lestes sp. Behavioural observations were conducted in a 2–1 arena and predation rate experiments in 1–1 jars in the laboratory.
• 2 Behavioural observations revealed that attack and capture efficiencies by Lestes were higher on smaller cladocerans (Polyphemus and Ceriodaphnia) than on other taxa. Small Lestes had little success ingesting the small ostracod Cypridopsis, whereas larger Lestes captured and ate it easily.
• 3 Predation-rate experiments showed that Lestes has a clear preference for smaller cladocerans over both a large cladoceran (Simocephatus) and all three ostracods (Cypricercus, Cyclocypris, and Cypridopsis). Most Lestes were unable to consume the larger Cypricercus.
• 4 Attack rates and predation rates were highly variable among individual predators.
• 5 These data indicate that damselfly larvae are size selective and consume all but very large cladocerans more readily than ostracods.

     

Carbon accumulation, distribution and water use of Danthonia richardsonii swards in response to CO2 and nitrogen supply over four years of growth

Microcosms of Danthonia richardsonii (Cashmore) accumulated more carbon when grown under CO₂ enrichment (719 μL L^–1 cf. 359 μL L^–1) over a four-year period, even when nitrogen availability severely restricted productivity (enhancement ratios for total microcosm C accumulation of 1.21, 1.14 and 1.29 for mineral N supplies of 2.2, 6.7 and 19.8 g N m^–2 y^–1, respectively). The effect of CO₂ enrichment on total system carbon content did not diminish with time. Increased carbon accumulation occurred despite the development over time of a lower leaf area index and less carbon in the green leaf fraction at high CO₂. The extra carbon accumulated at high CO₂ in the soil, senesced leaf and leaf litter fractions at all N levels, and in root at high-N, while at low-and mid-N less carbon accumulated in the root fraction at high CO₂. The rate of leaf turnover was increased under CO₂ enrichment, as indicated by increases in the carbon mass ratio of senesced to green leaf lamina. Microcosm evapotranspiration rates were lower at high CO₂ when water was in abundant supply, resulting in higher average soil water contents. The higher soil water contents at high CO₂ have important implications for microcosm function, and may have contributed significantly to the increased carbon accumulation at high CO₂. These results indicate that CO₂ enrichment can increase carbon accumulation by a simple soil–plant system, and that any increase in whole system carbon accumulation may not be evident from snapshot measurements of live plant carbon.     

Simultaneous cloning of multiple nuclear genes by pooling PCR products of variable size: a cost‐effective method of improving efficiency in large‐scale genetic analyses

I present a simple approach to overcome the high cost and low efficiency of cloning polymerase chain reaction (PCR) products for individuals in wide‐scale population genetic analyses. The methodology reduces the number of cloning reactions per individual by engineering a suite of genetic markers that differ in size and pooling these PCR products prior to cloning. Alleles from each gene are then recovered by screening transformed bacterial colonies and identifying the inserts corresponding to each gene based on size. I demonstrate the utility of this technique by presenting the results I obtained from cloning four nuclear genes in 118 individuals from three species of sea urchins (Strongylocentrotus purpuratus, S. droebachiensis and S. pallidus). Of the 472 different PCR products I cloned, I recovered at least one allele for 432 of them (91.5%) by screening between 16 and 32 bacterial colonies for each individual. There existed a bias with respect to recovery efficiency: the two largest fragments (1130–800 bp) were recovered 100% of the time, while the two smaller fragments (580–650 bp) were recovered in 85.6% and 81.4% of the experiments, respectively. I discuss the promise of this application for wide‐scale genetic analyses.     

A NEW SEA SPIDER (ARTHROPODA: PYCNOGONIDA) WITH A FLAGELLIFORM TELSON FROM THE LOWER DEVONIAN HUNSRÜCK SLATE, GERMANY

Abstract:  A new Lower Devonian sea spider (Arthropoda: Pycnogonida) from the Hunsrück Slate, Germany, is described as Flagellopantopus blocki gen. et sp. nov. This is only the sixth fossil pycnogonid species to be described. Its most remarkable and unique aspect is the long, flagelliform telson. Although our fossil apparently lacks chelifores (an apomorphy), the retained telson and the segmented trunk end behind the last pair of legs resolve F. blocki to a fairly basal position in the pycnogonid stem lineage. It probably lies between Palaeoisopus problematicus Broili, which has a lanceolate telson and the most trunk segments of any sea spider, and all other Silurian–Recent Pycnogonida. Our new material shows that at least two fossil pycnogonids retained a telson, albeit with very different morphologies, and further supports the idea that a greater diversity of body plans existed among the Palaeozoic pycnogonid taxa.     

Patterns of persistence and isolation indicate resilience to climate change in montane rainforest lizards

Globally, montane tropical diversity is characterized by extraordinary local endemism that is not readily explained by current environmental variables indicating a strong imprint of history. Montane species often exist as isolated populations under current climatic conditions and may have remained isolated throughout recent climatic cycles, leading to substantial genetic and phenotypic divergence. Alternatively, populations may have become contiguous during colder climates resulting in less divergence. Here we compare responses to historical climate fluctuation in a montane specialist skink, Lampropholis robertsi, and its more broadly distributed congener, L. coggeri, both endemic to rainforests of northeast Australia. To do so, we combine spatial modelling of potential distributions under representative palaeoclimates, multi‐locus phylogeography and analyses of phenotypic variation. Spatial modelling of L. robertsi predicts strong isolation among disjunct montane refugia during warm climates, but with potential for localized exchange during the most recent glacial period. In contrast, predicted stable areas are more widespread and connected in L. coggeri. Both species exhibit pronounced phylogeographic structuring for mitochondrial and nuclear genes, attesting to low dispersal and high persistence across multiple isolated regions. This is most prominent in L. robertsi, for which coalescent analyses indicate that most populations persisted in isolation throughout the climate cycles of the Pleistocene. Morphological divergence, principally in body size, is more evident among isolated populations of L. robertsi than L. coggeri. These results highlight the biodiversity value of isolated montane populations and support the general hypothesis that tropical montane regions harbour high levels of narrow‐range taxa because of their resilience to past climate change.     

Rapid,pervasive genetic differentiation of urban white‐footed mouse (Peromyscus leucopus) populations in New York City

We investigated genetic diversity and structure of urban white‐footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White‐footed mice are ‘urban adapters’ that occur at higher population densities as habitat fragments are reduced in area but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in 14 NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white‐footed mice as measured by pairwise F_ST, assignment tests, and Bayesian clustering analyses performed by Structure and baps . Analysis of molecular variance revealed that genetic differences between populations separated by a few kilometres are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation by distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.