Relict conifers from the mid-Pleistocene of Rhodes,Greece

The mid-Pleistocene Kolymbia Flora of Rhodes, Greece occurs in the Lindos Bay Clay facies group of the Rhodes Formation and was deposited in a marine setting at about a depth of 200 m. Recorded in the flora are the youngest presence of Glyptostrobus in the eastern Mediterranean, an extinct species of Pinus very similar to the modern relict Pinus canariensis, and a new species of the disjunct Cedrus. These taxa indicate that some relict plant taxa existed on Rhodes later than previously recognised. The late presence of Taxodiaceae in the eastern Mediterranean may demerit its usefulness for determining the Pliocene–Pleistocene boundary. The finding of Liquidambar, Zelkova and Fagus in the flora supports the idea of Rhodes, and possibly the eastern Mediterranean, as a refugium during the mid-Pleistocene. Similar fossil assemblages should be found in adjacent Turkey because the Lindos Bay Clay records an extensive marine transgression probably resulting from graben tectonics that lead to the ultimate separation of Rhodes from mainland Turkey.     

The fauna of Greece and adjacent areas in the Age of Homer: evidence from the first written documents of Greek literature

Aim To study the composition of fauna in Greece and adjacent areas around 3000 years ago based on the knowledge of Homeric man about the animal kingdom. Location Greece and adjacent areas. Method Analysis of information derived from a thorough study of the first written documents of Greek literature, the epics, attributed to Homer and Hesiod. Results Records of 2442 animals were found, corresponding to 71 different animal names. All animal names were attributed to recent taxa, at different category levels; the majority (65%) were assigned to taxa at the species level and the rest to supraspecific taxa. Most of the animal names recorded in the epics have been retained as integral words or roots in Modern Greek and they have been used in the formation of the Latin scientific taxa names. Five animal phyla appear in the texts: (1) Chordata (mostly birds and mammals), (2) Arthropoda, (3) Mollusca, (4) Porifera, and (5) Annelida. Information in the epics also includes morphology, biology, ecology (habitat and prey–predator relationships), and behaviour. The presence of several species in the area in that period is documented on the basis of archaeological and/or palaeontological findings from various Greek localities. Main conclusions The knowledge of Homeric man about animals, as reflected in the epics, seems to concentrate mainly, but not exclusively, on animals involved in human activities. The populations of some common animal species of the Homeric Age in Greek populated areas have become extinct or reduced at the present time. On the other hand, some common animals of the present time do not appear in the epics, since they were introduced later. Useful zoological information can be derived from the study of classical texts, which may help historical biogeographers as a supplement to archaeology and art, in the reconstruction of faunas of older periods.     

Life-history characters and phylogeny are correlated with extinction risk in the Australian angiosperms

Aim To determine whether life‐history characters that affect population persistence (e.g. habit and life span) and those that influence reproductive success (e.g. sexual system and fruit type) are non‐randomly correlated with extinction risk (i.e. threat category) in the Australian flora (c. 19,000 species, of which c. 14% is threatened). To identify patterns that present useful conservation directions. To understand patterns of extinction risk in the Australian flora at a broad scale. Location Continental Australia. Methods A country‐wide exploration of four life‐history characters in the Australian flora (n = 18,822 species) was undertaken using reference texts, expert opinion, herbarium records and field work. For each character and threat‐category combination, a G‐test (using a log‐linear model) was performed to test the null hypothesis that the two factors were independent in their effects on count. A generalized linear model (GLM) with a logit link and binomial error distribution was constructed with the proportion of taxa in each extinction risk category as the response variable and the habit, sex and fruit‐type characters as explanatory terms. In a separate approach, we investigated patterns across the threat categories of non‐endangered extant, endangered, and extinct using a multinomial model. We examined whether or not species‐poor genera were more likely to contain threatened or extinct species than species‐rich genera. A GLM with a binomial error distribution and logit link function was constructed to obtain a weighted regression on the proportion of species listed as extinct or endangered within a genus versus the log of the size of the genus. We also used a supertree analysis and character tracing to investigate the role of phylogeny on extinction risk. Results We found that the Australian flora is primarily composed of bisexual shrubs with dry‐dehiscent fruits. Dioecious breeding systems (separate female and male flowers on separate plants) in many floras are the predominant unisexual system, but in Australia there are unexpectedly high levels of monoecy (separate female and male flowers on the same plant). Within the extinct data set of 31 species we detected a significant departure from that expected for habit but not for life span, sexual system or fruit type. There are significantly fewer trees on the extinct list than expected. This may reflect the greater resilience of trees than of other growth habits to extinction processes as well as the observation time‐frame. Within the endangered data set of 450 species we found significant differences in the representation of the observed characters from that expected within sex systems and fruit types. We show that, depending on the life form, unisexual breeding systems can be significantly and positively associated with endangered species compared with non‐threatened species. For example, there are more monoecious species than expected by chance among the tree species listed as endangered but fewer among the herbaceous life forms. Threat category was found to be non‐randomly clustered in some clades. Main conclusions Life‐history characters in certain combinations are predictive of extinction risk. Phylogeny is also an important component of extinction risk. We suggest that specific life‐history characters could be used for conservation planning and as an early warning sign for detecting vulnerability in lists of species.     

Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises

In isolated oceanic islands, colonization patterns are often interpreted as resulting from dispersal rather than vicariant events. Such inferences may not be appropriate when island associations change over time and new islands do not form in a simple linear trend. Further complexity in the phylogeography of ocean islands arises when dealing with endangered taxa as extinctions, uncertainty on the number of evolutionary ‘units’, and human activities can obscure the progression of colonization events. Here, we address these issues through a reconstruction of the evolutionary history of giant Galápagos tortoises, integrating DNA data from extinct and extant species with information on recent human activities and newly available geological data. Our results show that only three of the five extinct or nearly extinct species should be considered independent evolutionary units. Dispersal from mainland South America started at approximately 3.2 Ma after the emergence of the two oldest islands of San Cristobal and Española. Dispersal from older to younger islands began approximately 1.74 Ma and was followed by multiple colonizations from different sources within the archipelago. Vicariant events, spurred by island formation, coalescence, and separation, contributed to lineage diversifications on Pinzón and Floreana dating from 1.26 and 0.85 Ma. This work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human‐mediated dispersal events and highlights the need to take into account both vicariance and dispersal when dealing with organisms from islands whose associations are not simply explained by a linear emergence model.     

ANCESTRAL CHARACTER ESTIMATION UNDER THE THRESHOLD MODEL FROM QUANTITATIVE GENETICS

Evolutionary biology is a study of life's history on Earth. In researching this history, biologists are often interested in attempting to reconstruct phenotypes for the long extinct ancestors of living species. Various methods have been developed to do this on a phylogeny from the data for extant taxa. In the present article, I introduce a new approach for ancestral character estimation for discretely valued traits. This approach is based on the threshold model from evolutionary quantitative genetics. Under the threshold model, the value exhibited by an individual or species for a discrete character is determined by an underlying, unobserved continuous trait called “liability.” In this new method for ancestral state reconstruction, I use Bayesian Markov chain Monte Carlo (MCMC) to sample the liabilities of ancestral and tip species, and the relative positions of two or more thresholds, from their joint posterior probability distribution. Using data simulated under the model, I find that the method has very good performance in ancestral character estimation. Use of the threshold model for ancestral state reconstruction relies on a priori specification of the order of the discrete character states along the liability axis. I test the use of a Bayesian MCMC information theoretic criterion based approach to choose among different hypothesized orderings for the discrete character. Finally, I apply the method to the evolution of feeding mode in centrarchid fishes.     

An updated checklist of the vascular flora alien to Italy

An updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented. The checklist includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms, and 1551 angiosperms. 157 taxa are archaeophytes and 1440 neophytes. The alien taxa currently established in Italy are 791 (570 naturalized and 221 invasive), while 705 taxa are casual aliens, 4 are not assessed, 7 are of unknown regional distribution, 47 have not been confirmed in recent times, 3 are considered extinct or possibly extinct in the country, and 40 are doubtfully occurring in Italy. This checklist allows to establish an up-to-date number (9792) of taxa constituting the whole (native and alien) Italian flora.     

Diatom flora of surface sediments of the Amur River Estuary and adjacent areas of the Sea of Japan and the Sea of Okhotsk

Results of the study of the diatom flora from surface sediments of the Amur River Estuary and adjacent areas of the Sea of Japan and the Sea of Okhotsk are presented for the first time. This study revealed high species diversity of diatoms: 287 diatom taxa belonging to 80 genera were identified in 35 surface sediment samples. The ecological composition of diatom assemblages allowed us to evaluate the influence of the Amur River runoff on adjacent areas of the seas.     

An updated checklist of the vascular flora native to Italy

An updated inventory of the native vascular flora of Italy, providing details on the occurrence at regional level, is presented. The checklist includes 8195 taxa (6417 species and 1778 subspecies), distributed in 1092 genera and 152 families; 23 taxa are lycophytes, 108 ferns and fern allies, 30 gymnosperms and 8034 angiosperms. The taxa currently occurring in Italy are 7483, while 568 taxa have not been confirmed in recent times, 99 are doubtfully occurring in the country and 19 are data deficient. Out of the 568 not confirmed taxa, 26 are considered extinct or possibly extinct.     

Patterns of endangerment in the hawaiian flora

The Hawaiian flora, because of its great isolation, high levels of endemism, known lineages, and high rates of endangerment, offers unique opportunities to explore patterns of endangerment related to phylogeny, ecological and life history traits, and geographic patterns. Nine percent of the native flora of 1159 taxa are already extinct, and 52.5% are at risk (extinct, endangered, vulnerable, or rare). Risk is strongly associated with limited geographic distribution at several scales: endemic taxa (native only to the Hawaiian Islands) are at far greater risk than indigenous taxa (with both Hawaiian and extra-Hawaiian ranges); single-island endemics are more at risk than multi-island endemics; small islands have the highest proportion of endemic taxa at risk; and endemics with more limited habitat distributions (elevation, community type) are more at risk. Historic population density is a strong predictor of risk, and taxa with low historic population densities are at greatest risk with rapid anthropogenic changes. Among the major islands, Maui Nui has the highest percent of taxa that are extinct. Kaua'i has the lowest percent of extinct taxa and the highest proportion of single-island endemic taxa that are rare. Endemic taxa at risk are associated with distributions in shrublands, forests, bogs, and cliff habitats. Endemic taxa with distributions in low elevation dry habitats have the highest proportion of taxa at risk, but the greatest absolute numbers of taxa at risk have distributions in mesic lowland and montane forests, and in wet montane forests. The life history patterns associated with risk are complicated, and inclusion of the effects of evolutionary relationships (lineages) changes some of these patterns. Species level analyses without respect to lineage shows risk associated with monomorphic (hermaphroditic) breeding systems and bird pollination because of the large number of hermaphroditic, bird-pollinated species in the Campanulaceae. Analyses incorporating the effect of lineage greatly reduce the impact of large lineages and result in an association of risk with insect pollination, and no effect of breeding system. There is no association of lineage size and the percent of taxa at risk within the lineage; endemic taxa from lineages with large radiations are at no greater risk than endemic single-taxon lineages. The percentages of taxa at risk at the family level in the Hawaiian Islands and worldwide (excluding Hawaiian taxa) are positively correlated, although flowering plant families in the Hawaiian Islands have a much greater proportion of taxa at risk. Some of the approaches described here may be useful to predict geographical and biological patterns of endangerment in island and island-like ecosystems under increasing pressures of endangerment and extinction.     

Fingerprints of environmental change on the rare mediterranean flora: a 115-year study

We empirically assessed the long‐term changes in the rare species assemblage of a Mediterranean flora, in terms of species life history traits, niche and biogeographic features, and taxonomic groups. We used a 115‐year historical record of ca. 2100 plant species occurrences in a 6250 km² region in Mediterranean France. Species were assigned to two classes of regional abundance for the years 1886 and 2001 (rare species, i.e. exhibiting one or two occurrences vs. nonrare species), and to three classes of abundance changes during 1886–2001 (decreasing/extinct, stable, increasing/immigrant). Then, we tested whether species regional abundance and species abundance change were related to their morphological and life‐history traits (life form, perenniality, height, dispersal agent, pollination mode), niche and biogeographic features (habitat specialization, level of endemism, biogeographic origin) and taxonomic group. The regional assemblage of rare species was not biologically random and significantly changed between 1886 and 2001. Species classified as rare in 1886 had a significantly higher rate of extinction in the study region during 1886–2001. The highest rate of regression/extinction was found among hydrophyte and/or water‐dispersed rare species, and among annual rare species. However, herbaceous perennial, tree and wind‐dispersed rare species significantly increased in abundance during 1886–2001. Rare species with Eurosiberian distributions, occurring at the southern margin of their range in the study region, dramatically declined or went extinct in the region during 1886–2001; whereas rare species with Mediterranean affinities remained significantly stable. We also found strong evidence for taxonomic patterns in species abundance and abundance changes from 1886 to 2001. The long‐term biological changes documented here in the rare species assemblage of a Mediterranean flora are consistent with the predicted consequences of climate and land use changes currently occurring in the Mediterranean Basin. With the potential decline or even extinction of entire taxa and the loss of southern ecotypes of widespread Eurosiberian species, both evolutionary history and speciation potential of the Mediterranean Region could be strongly altered in future decades.     

Towards integrated conservation of Australian endangered plants—the Western Australian model

Four percent of the Australian flora is rare and endangered with over 100 taxa presumed extinct. Western Australia contains a large proportion of the endangered flora of Australia with 238 taxa in a critical state of conservation and 70 species presumed extinct. Kings Park and Botanic Garden in south-west Australia is responsible for developing specialized collections of rare and endangered indigenous flora. Macro-and micropropagation procedures are used including conventional cutting and seed propagation, grafting and in thein vitro programme whole seeds (asymbiotic and symbiotic germination), excised seed embryos, shoot apices and inflorescence sections. Wherever possible explants are collected from major provenances of the species and a wide cross section of a species population. Although many of the rare flora of Western Australia are now in theex situ collection maintained by Kings Park and Botanic Garden attempts are being made to develop slow growth storage forin vitro cultures and cryostorage. Trial recovery programmes have commenced with a number of species including the rare and endangered Purdie's donkey orchid (Diuris purdiei). Results of these recovery programmes will guide future efforts in conserving and recovering rare Australian species.     

Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record

A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (< 5 kg) for the ancestors of those clades. When the temporal information associated with fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of directional trends, thereby yielding more reliable ancestral character state reconstructions.     

Fossils, molecules, divergence times, and the origin of lissamphibians

A review of the paleontological literature shows that the early dates of appearance of Lissamphibia recently inferred from molecular data do not favor an origin of extant amphibians from temnospondyls, contrary to recent claims. A supertree is assembled using new Mesquite modules that allow extinct taxa to be incorporated into a time-calibrated phylogeny with a user-defined geological time scale. The supertree incorporates 223 extinct species of lissamphibians and has a highly significant stratigraphic fit. Some divergences can even be dated with sufficient precision to serve as calibration points in molecular divergence date analyses. Fourteen combinations of minimal branch length settings and 10 random resolutions for each polytomy give much more recent minimal origination times of lissamphibian taxa than recent studies based on a phylogenetic analyses of molecular sequences. Attempts to replicate recent molecular date estimates show that these estimates depend strongly on the choice of calibration points, on the dating method, and on the chosen model of evolution; for instance, the estimate for the date of the origin of Lissamphibia can lie between 351 and 266 Mya. This range of values is generally compatible with our time-calibrated supertree and indicates that there is no unbridgeable gap between dates obtained using the fossil record and those using molecular evidence, contrary to previous suggestions.     

Morphometric variation in the hominoid orbital aperture: a case study with implications for the use of variable characters in Miocene catarrhine systematics

Variable characters are ubiquitous in hominoid systematics and present a number of unique problems for phylogenetic analyses that include extinct taxa. As yet, however, few studies have quantified ranges of variation in complex morphometric characters within extant taxa and then used those data to assess the consistency with which discrete character states can be applied to poorly represented fossil species. In this study, ranges of intrageneric morphometric variation in the shape of the hominoid orbital aperture are estimated using exact randomization of average pairwise taxonomic distances (ATDs) derived from size-adjusted centroid, height-width, and elliptic Fourier (EF) variables. Using both centroid and height-width variables, 19 of the 21 possible ATDs between individuals representing seven extinct catarrhine taxa (Aegyptopithecus, Afropithecus, Ankarapithecus, Ouranopithecus, Paranthropus, Sivapithecus and Turkanapithecus) can be observed within a single extant hominoid subspecies, although generally with low probabilities. A resampling study is employed as a means for gauging the effect that this intrataxonomic variation may have on the consistency with which discrete orbital shape character states can be delimited given the small sample sizes available for most Miocene catarrhine taxa preserving this feature (i.e., n=1). For each type of morphometric variable, 100 cluster (UPGMA) analyses of pairwise ATDs are performed in which a single individual is randomly selected from each hominoid genus and analyzed alongside known extinct taxa; consensus trees are computed in order to obtain the frequencies with which different shape clusters appeared in each of the three analyses. The two major clusters appearing most frequently in all three consensus trees are found in only 57% (centroid variables), 49% (height-width variables), and 36% (EF variables) of these trees. If ranges of variation within represented extinct taxa could also be estimated, these frequencies would certainly be far lower. Hominoids clearly exhibit considerable intrageneric, intraspecific, and even intrasubspecific variation in orbit shape, and substantial morphometric overlap exists between taxa; consequently, discrete character states delimiting these patterns of continuous variation are likely to be highly unreliable in phylogenetic analyses of living and extinct species, particularly as the number of terminal taxa increases. Morphological phylogenetic studies of extant catarrhines that assess the effect of different methods (e.g., use of objective a priori weighting or frequency coding of variable characters, inclusion vs. exclusion of variable characters, use of specific vs. supraspecific terminal taxa) on phylogenetic accuracy may help to improve the techniques that systematists employ to make phylogenetic inferences about extinct taxa.     

Floristic corridors for moss distribution across the Neovolcanic Belt of Mexico. I. The Tuxpan corridor

Abstract

In theory, the E-W location and high elevation of the Neovolcanic Belt have reduced floristic flow between parts of northern and southern Mexico. However, this barrier effect is not complete, as may be inferred from the distribution of moss taxa in adjacent areas. Migration across the Neovolcanic Belt may account for the presence of many moss species on either side of this mountain range. Moss exchange may take place through topographic discontinuities herewith designated as floristic corridors. There are at least seven such inland corridors as well as the two coastal plain areas. The latter are probably very important in the latitudinal distribution of lowland species from the tropics northward. The moss flora of the Tuxpan corridor in Michoacan includes lowland species and corridor taxa which have reached or crossed the Neovolcanic Belt from the south if of tropical derivation. The remaining mosses are high elevation species or taxa of broad altitudinal distribution which have spread along the mountains.     

Evolution of bird communities in the Neogene of Central Asia,with a review of the Neogene fossil record of Asian birds

A complete taxonomic review of Neogene birds of continental Asia is provided. To date, avifauna from the latter half of the Miocene and Pliocene of Central Asia (Mongolia and adjacent regions of Inner Asia) are most thoroughly investigated. Available data enable a reconstruction of successive replacement of Early and Middle Miocene avifaunas by communities of the Recent type. Middle Miocene avifaunas of Mongolia include a great number of extinct genera and species, many of which were widespread in Eurasia. Extant genera became dominant in the Late Miocene and taxa close to living species appear in the Late Pliocene fossil record. Late Pliocene communities of birds of Central Asia were complex in genesis, composed of Miocene relicts (Struthio), immigrants from the European regions of the Palearctic (phasianid Plioperdix), North American immigrants (Calcarius), and also autochthonous elements, the origin of which is apparently connected with the arid belt of Central Asia (diverse passerines).     

Large-scale sequencing and the new animal phylogeny

Although comparisons of gene sequences have revolutionised our understanding of the animal phylogenetic tree, it has become clear that, to avoid errors in tree reconstruction, a large number of genes from many species must be considered: too few genes and stochastic errors predominate, too few taxa and systematic errors appear. We argue here that, to gather many sequences from many taxa, the best use of resources is to sequence a small number of expressed sequence tags (1000-5000 per species) from as many taxa as possible. This approach counters both sources of error, gives the best hope of a well-resolved phylogeny of the animals and will act as a central resource for a carefully targeted genome sequencing programme.     

铜仁市万山特区木本植物区系研究

经野外调查统计,铜仁市万山特区共有木本植物82科216属495种（包括种下等级,下同）。其中,裸子植物5科6属7种;被子植物77科210属488种,包括单子叶植物3科7属17种,双子叶植物74科203属471种。区系分析结果表明：（1）区系地理成分复杂多样,温带性质明显,同时与热带区系联系紧密;（2）区系性质具有原始性,有古老和孑遗类群;（3）特有现象明显,表现为中国特有种数量较多;（4）与邻近6个地区的木本植物区系比较可知,万山特区与重庆大木山关系密切,与泸沽湖较疏远。     

泗洱自然保护区种子植物区系特征分析

在对泗洱自然保护区详细调查的基础上,对其种子植物的科、属的分布区类型进行了统计分析。结果表明：(1)保护区内种子植物类群丰富;(2)优势科、属明显;(3)区系起源古老;(4)地理成分复杂;(5)种子植物区系在科和属级水平上均显示出温带性质,同时泛热带类型丰富;(6)保护区内植被具明显的过渡性质;(7)分化现象明显,中间类型和特有种丰富。     

外群选择对隧蜂科（膜翅目：蜜蜂总科）系统重建的影响

外群用于给树附根和推断祖先性状状态。通常,来自内群的姐妹群中的多个分类单元被共同选择作为外群。为了在经验上验证这一方法, 我们采用了3种外群选择策略： 姐妹群中的单一分类单元, 姐妹群中的多个分类单元和连续姐妹群中的多个分类单元。以隧蜂科（膜翅目： 蜜蜂总科）的系统发育重建为例, 我们评估了这3种策略对树拓扑结构的影响, 包括最大似然树、 最大简约树和贝叶斯树。初步结果表明： 相比其他两种策略, 采用姐妹群中的多个分类单元作为外群更有利于系统发育重建得到现已被广泛认可的隧蜂科系统发育关系; 相比最大似然法和贝叶斯法, 虽然隧蜂科系统发育关系没有被很好地解决, 但最大简约法在不同外群选择策略下得到了较为一致的拓扑结构