Mexical plant phenology: is it similar to Mediterranean communities?

The sclerophyllous, evergreen vegetation found in Mexico under tropical climate is named 'Mexical' (MEX) and presents many traits that have been thought to converge under a Mediterranean climate. Flowering phenology is strongly similar across Mediterranean-type ecosystems (MTEs) and this paper investigates MEX plant phenology in this context. The common history of the vegetation and the differences in the climatic conditions experienced by MEX and MTE taxa provide an ideal scenario to infer the relative importance of natural selection and historical constraints in the phenological response of plants to climatic conditions. This study has involved collecting field and bibliographic data on flowering phenology of MEX communities to detect (1) similarities at the community level between MTEs and MEX, (2) similarities between Tertiary and Quaternary taxa in MTEs and MEX, and (3) similarities between congeneric taxa from MEX and MTEs (taxa sharing a common ancestor but having evolved under different climates). Flowering in MEX does not occur mainly in spring, as in MTEs, but in summer, suggesting a response that maximizes water use in the rainy season. Flowering phenology of MEX species differed from their MTE congeneric species, suggesting that even though a common ancestor is shared, environmental pressures have led to different phenological responses in MEX and MTE plants. The flowering season for species that originated in the Tertiary and Quaternary did not differ in MEX, as expected, because of climatic uniformity along the whole time line. In MTEs, flowering differences between Tertiary and Quaternary species were not congruent, suggesting that the balance between the historical constraints and the selective force of the Mediterranean climate is different among the three MTEs, and a particular explanation is needed for each. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 297–303.     

Evolution, origin and age of lineages in the Californian and Mediterranean floras

This paper addresses some of the conceptual issues involved in the analysis of the age and origin of mediterranean‐climate plant taxa, paying particular attention to three topics: (1) the importance of an explicit time frame in the definition of biogeographical origins, (2) the distinction between the age of traits and the age of taxa, and (3) the idea of mediterranean‐type ecosystems as environmental islands. (1) In California, recent analyses demonstrate that the diversity of species derived from different biogeographical origins is significantly correlated with temperature and precipitation gradients. These patterns support the hypothesis that niche conservatism is an important factor structuring modern diversity gradients. However, depending on how far back in time one looks, a species may be assigned to different origins; future discussions of biogeographical origins need to address the appropriate time frame for analysis. (2) Past research has demonstrated distinctive trait syndromes among woody plants of the Mediterranean, Chile, California and Mexico, and proposed that the syndromes are associated with lineages of different age in these floras. Reanalysis of individual traits demonstrates greater variability among regions than previously reported. The classification of plants into ‘old’ and ‘new’ genera is re‐evaluated, and it is suggested that greater attention be paid to the age of traits, rather than to the age of taxa, especially at an arbitrary rank such as genus. (3) The idea of mediterranean‐climate regions as ‘climatic islands’ is examined. Space–time diagrams of climate enable one to view the emergence of distinctive climatic regions in a continental context. The terms ‘synclimatic’ and ‘anticlimatic’ are proposed, referring to migration routes that parallel climate contours in space and time versus those that cross contours (including the case of geographic stasis in the face of climate change), respectively. Mediterranean‐climate regions have served as important case studies in plant ecology and evolution, and merit continued close examination in the light of continued advances in phylogenetics and palaeoecology.     

Molecular phylogeography of four endemic Sagittaria species (Alismataceae) in the Sino‐Japanese Floristic Region of East Asia

To reveal the role of climate oscillations of the Quaternary in forming the contemporary plant diversity in the temperate Sino‐Japanese Floristic Region of mainland China, we assess the phylogeographical patterns of four Sagittaria species in the region using sequence data from plastid DNA non‐coding regions (psbA‐trnH, the rpl16 intron and trnC‐ycf6) and the internal transcribed spacers of nuclear ribosomal DNA (nrITS). Based on both datasets, the divergence time among the four studied species was estimated to fall in the Late Tertiary (plastid DNA: 7.1–13.7 Mya; ITS: 11.1–16.1 Mya). The ancestral distribution analyses revealed that regions with a great diversity in topography, climate and ecological conditions, e.g. the Hengduan Mountains, Central China and East China, were the areas where the endemics originated. Mismatch distribution analyses revealed that each species had experienced a range expansion in response to Quaternary climatic oscillations. Our findings contradict the hypothesis of Quaternary origins of the endemic Sagittaria spp.; we support the view that modern species in the Northern Hemisphere originated mostly during the Tertiary. Range expansion may have profoundly modified the current distribution ranges of Sagittaria species in the Sino‐Japanese Floristic Region. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 6–20.     

Refugia within refugia – patterns in endemism and genetic divergence are linked to Late Quaternary climate stability in the Iberian Peninsula

In Europe, southern peninsulas served as major refugia during Pleistocene cold periods. However, growing evidence has revealed complex patterns of glacial survival within these southern regions, with multiple glacial refugia within each larger refugial area. We investigated the extent to which patterns of endemism and phylogeographic are concordant across animal species in the Iberian Peninsula, one of the most important unglaciated areas in Europe during the Pleistocene, can be explained in terms of climatic stability. We found that historical climatic stability (notably climate velocity measures integrating macroclimatic shifts with local spatial topoclimate gradients) was often among the most important predictors of endemic species richness for different taxonomic groups using models that also incorporated measures of modern climate. Furthermore, for some taxonomic groups, climatic stability was also correlated with patterns of spatial concordance in interpopulation genetic divergence across multiple taxa, and private haplotypes were more frequently found in relatively stable areas. Overall, our results suggest that both endemism patterns and cross‐taxa concordant phylogeographic patterns across the Iberian Peninsula to some extent are linked to spatial variation in Late Quaternary climate stability, in agreement with the proposed ‘refugia‐within‐refugia’ scenario. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 13–28.     

Climate Analysis of Endemic Species-A Novel Method for Quantitative Analysis of Global Climate Change Since Tertiary

There are many extant endemic plants in China, which were widely distributed in the North Hemisphere during Tertiary. The global cooling during the Tertiary caused a series of narrow distribution regions of the plants. Quaternary glaciation invaded most regions of North America and Eurasia where severe destruction was imposed onto vegetation. However, such destruction was lessened in China largely because of specific topographic and geographical and obviously, a number of other conditions accounted for an unusual refugee camp for the relics of plants in China, among which lots of endemic taxa exist. Recently, Chinese endemic species, such as Metaseqouia, Eucommia , have been employed to conduct multi-disciplinary comprehensive studies so as to analyze Tertiary climate changes quantitatively. Meanwhile, a rigorous method, i.e. climate analysis of endemic species (CAES) has come to maturation. This method is characteristic of some generality because it is supposed to be applicable to the endemic species in other regions of the world. CAES is involved in the following aspects: 1. Conduct multidisciplinary studies on living and fossil species of endemic plants and trace their evolutionary courses. 2. Compare fossil species with living one and clarify which is the nearest living relative (NLR) to fossil counterpart. 3. Fossils and their living counterparts (NLR) are supposed to have similar ecological requirements to meet their life cycles. 4. Investigate the geographic distribution of living and fossil plants within the same taxa and ascertain the dynamic changes of their distributions in geological age. 5. Analyze climate factors in the distribution of specific endemic taxa and obtain the data of climatic characters which are suitable for reconstruction of paleoclimate where fossil counterparts lived. 6. Further study the physio-ecology of living species and determinate paleoclimate where fossil counterparts lived. 7. Integrate analysis of the data from steps 4, 5 and 6, and quantitatively reconstruct the climate where fossil and living plants survive.     

定量分析第三纪以来环境变化的新方法：—特有种气候分析法

1　全球气候变化研究新动向自 2 0世纪 80年代以来 ,全球气候变化研究至今仍方兴未艾。全球气温波动、大气中温室气体丰度变化、气候格局改变、气候带迁移和降水量增减 ,都影响到社会经济的发展和人类生活质量的提高。各国政府对全球气候变化的研究 ,如气候演变的过程、短期和长期气候变化的预测和自然灾害的防治都给予极大关注和财力支持[1] 。目前全球气候变化的研究正向两个方向发展。1.1　加大全球气候变化研究时间尺度 ,从研究当今气候发展到研究地质历史时期气候变化全球气候变化 ,如大气中ＣＯ2 浓度的变化、温度的升降和降水量的变…     

定量分析第三纪以来环境变化的新方法——特有种气候分析法

There are many extant endemic plants in China, which were widelydistributed in the North Hemisphere during Tertiary. The global cooling during the Tertiary caused a series of narrow distribution regions of the plants. Quaternary glaciation invaded most regions of North America and Eurasia where severe destruction was imposed onto vegetation. However, such destruction was lessened in China largely because of specific topographic and geographical and obviously, a number of other conditions accounted for an unusual refugee camp for the relics of plants in China, among which lots of endemic taxa exist. Recently, Chinese endemic species, such as Metaseqouia, Eucommia, have been employed to conduct multi-disciplinary comprehensive studies so as to analyze Tertiary climate changes quantitatively. Meanwhile, a rigorous method, i.e. climate analysis of endemic species (CAES) has come to maturation. This method is characteristic of some generality because it is supposed to be applicable to the endemic species in other regions of the world. CAES is involved in the following aspects: 1. Conduct multidisciplinary studies on living and fossil species of endemic plants and trace their evolutionary courses. 2. Compare fossil species with living one and clarify which is the nearest living relative (NLR) to fossil counterpart. 3. Fossils and their living counterparts (NLR) are supposed to have similar ecological requirements to meet their life cycles. 4. Investigate the geographic distribution of living and fossil plants within the same taxa and ascertain the dynamic changes of their distributions in geological age. 5. Analyze climate factors in the distribution of specific endemic taxa and obtain the data of climatic characters which are suitable for reconstruction of paleoclimate where fossil counterparts lived. 6. Further study the physio-ecology of living species and determinate paleoclimate where fossil counterparts lived. 7. Integrate analysis of the data from steps 4, 5 and 6, and quantitatively reconstruct the climate where fossil and living plants survive.     

Differing evolutionary patterns underlie convergence on elongate morphology in endemic fishes of Lake Waccamaw, North Carolina

An extensive body of research has recently demonstrated patterns of parallel and/or convergent evolution that arise from divergent natural selection pressures exerted across environmental gradients. These studies, although providing some of our best empirical evidence for natural selection, have focused on rather narrow phylogenetic scopes, more often than not comparing patterns of morphological change among closely‐related taxa within a single genus. Organisms in replicated populations in these studies are often assumed to have accomplished convergence via similar underlying processes. However, such assumptions cannot be made when looking at evolution across broader phylogenetic and ecological spectra. In the present study, we assessed morphological change across a much broader scale to test whether similar evolutionary and developmental patterns underlie convergence. Specifically, we studied morphological change that has occurred in a novel lake environment (Lake Waccamaw, North Carolina, USA) where three phylogenetically‐disparate fishes representing different orders have speciated and independently evolved streamlined morphologies relative to their deeper‐bodied progenitors occupying nearby streams and coastal regions. Geometric morphometric analyses revealed that, although the bulk of shape change between environments is similar across taxa, significant species‐specific responses, concordant with differing expectations based on the ecologies of these taxa, were also found. Moreover, allometry analyses indicated that the developmental patterns underlying this change also differ across taxa. The present study provides evidence that, within a common environment, convergence can be achieved by different evolutionary and developmental patterns in phylogenetically‐ and ecologically‐disparate taxa. Finally, these results contradict the commonly‐held hypothesis that fishes should be more streamlined in streams than lakes and emphasize the need to also consider other environmental characteristics, such as water clarity and physical complexity, in studies of divergence. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 636–645.     

Phylogenetic relationships between parthenogens and their sexual relatives: the possible routes to parthenogenesis in animals

In theory, parthenogenetic lineages have low evolutionary potential because they inexorably accumulate deleterious mutations and do not generate much genotypic diversity. As a result, most parthenogenetic taxa occupy the terminal nodes of phylogenetic trees. The rate and mode of development of parthenogenesis are important factors to consider when assessing its costs and benefits since they determine both the level of genetic diversity and the ecological adaptability of the resulting lineages. The origin of parthenogenesis is polyphyletic in many taxa, suggesting that genetic systems maintaining sexuality are often labile. In addition, the loss of sex may be achieved in several ways, leading to parthenogenetic lineages with distinct genetic profiles. This could then influence not only the fate of such lineages in the long term, but also the outcome of competition with their sexual counterparts in the short term. In this paper, we review the possible evolutionary routes to parthenogenesis based on a survey of the phylogenetic relationships between sexual and parthenogenetic lineages in a broad range of animals. We also examine the different mechanisms by which parthenogenetic lineages could arise, and discuss the influence of these mechanisms on both the genetic properties and the ecological life styles of the resulting lineages.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 151–163.     

An ecological tardis: the implications of facilitation through evolutionary time

It is often challenging to link ecological processes to evolution because different temporal scales are studied and necessarily inferred. In a recent paper by Valiente-Banuet et al., Quaternary plant taxa are shown to 'pull' more ancient Tertiary taxa through evolutionary time by facilitation. This finding has profound implications for population and community ecology. Positive species interactions are of wider importance than was assumed previously in determining community composition by enhancing long-term biodiversity, mediating climate change and providing an interdependent set of selection processes in addition to the environment. Future experiments should consider the evolutionary history of species, manipulate species interactions explicitly to test for environmental effects and re-evaluate the adaptive significance of traits in the context of other species.     

Phylogenetic perspective on ecological niche evolution in american blackbirds (Family Icteridae)

Analysis of ecological characters on phylogenetic frameworks has only recently appeared in the literature, with several studies addressing patterns of niche evolution, generally over relatively recent time frames. In the present study, we examined patterns of niche evolution for a broad radiation of American blackbird species (Family Icteridae), exploring more deeply into phylogenetic history. Within each of three major blackbird lineages, overlap of ecological niches in principal components analysis transformed environmental space varied from high to none. Comparative phylogenetic analyses of ecological niche characteristics showed a general pattern of niche conservatism over evolutionary time, with differing degrees of innovation among lineages. Although blackbird niches were evolutionarily plastic over differing periods of time, they diverged within a limited set of ecological possibilities, resulting in examples of niche convergence among extant blackbird species. Hence, an understanding of the patterns of ecological niche evolution on broad phylogenetic scales sets the stage for framing questions of evolutionary causation, historical biogeography, and ancestral ecological characteristics more appropriately.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 869–878.     

Phylogenetics, zoogeography, and the role of dispersal and vicariance in the evolution of the Rana catesbeiana (Anura: Ranidae) species group

The Rana catesbeiana species group consists of seven species, each variously distributed across eastern North America. We estimated the evolutionary relationships among 31 exemplars and used the phylogenetic hypothesis to examine the potential modes of speciation and relative role of dispersal in the evolution and zoogeography of this species group. Phylogenetic relationships based on 1554 combined base pairs of the cytochrome b and ND2 mitochondrial genes suggest that the species are closely related, having undergone rapid radiation from a common ancestor during the late Miocene or Pliocene. A Pleistocene origin for the rare R. okaloosae is suggested by its pattern of paraphyly with R. clamitans and by its geographically restricted distribution, although hybridization as the explanation for paraphyly cannot be ruled out. Dispersal–vicariance analysis suggested a Coastal Plain biogeographical region origin of the species group, supporting the notion that the region was an important centre of anuran diversification, with post-speciation dispersal playing a major role in explaining the distribution of the widespread species, R. catesbeiana , R. clamitans, and R. septentrionalis . High sea levels during the late Tertiary, greatly reducing and insularizing parts of the southern Coastal Plain region may have played a major role in the diversification of this group.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 601–624.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia

The evolutionary history and biogeography of freshwater-dependent taxa in Australia is of intrinsic interest given the present-day aridity of this continent. Cherax is the most widespread and one of the most species-rich of Australia's nine freshwater crayfish genera. The phylogenetic relationships amongst 19 of the 23 Australian Cherax were established from mitochondrial DNA sequences representing the 12S rRNA and 16S rRNA gene regions. The relationships among species support an initial east–west separation, followed by a north–south divergence in eastern Australia. Molecular clock estimations suggest that these divergences date back to the Miocene. The phylogenetic relationships support endemic speciation within geographical regions and indicate that long-distance dispersal has not led to recent speciation as previously hypothesized. This new evolutionary scenario is consistent with the climatic history of Australia and the evolutionary history of other similarly distributed freshwater-dependent organisms in Australia.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 553–563.     

Facultative apomixis and hybridization in arctic Potentilla section Niveae (Rosaceae) from Svalbard

The degree of sexual seed set and the ability to cross were investigated in three taxa of Potentilla section Niveae ( P. chamissonis , P. insularis and P. nivea ) from the Svalbard Archipelago. Emasculated and bagged flowers had little or no seed set, while 71% of the emasculated, bagged and pollinated flowers had some. The taxa are interpreted as pseudogamous apomicts. Parental plants and offspring were subjected to isozyme analysis. Most of the offspring were clones of the mother plant, but 1.7% had bands from the pollen donor. The sexual offspring were all produced by mother plants of P. insularis , which is interpreted as a facultative apomict. Surprisingly, crosses between different taxa gave higher seed to ovule ratios and numbers of sexually produced offspring than crosses within taxa. Some of the sexually produced hybrid offspring had the same kind of hairs on the petioles as their mother taxon, showing that hybrids may not be intermediate in hair characters, which are considered important in the delimitation of these taxa. The results of the present study indicate very close relationships among the investigated plants.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 373−381.     

The origin of snakes (Serpentes) as seen through eye anatomy

Snakes evolved from lizards but have dramatically different eyes. These differences are cited widely as compelling evidence that snakes had fossorial and nocturnal ancestors. Their eyes, however, also exhibit similarities to those of aquatic vertebrates. We used a comparative analysis of ophthalmic data among vertebrate taxa to evaluate alternative hypotheses concerning the ecological origin of the distinctive features of the eyes of snakes. In parsimony and phenetic analyses, eye and orbital characters retrieved groupings more consistent with ecological adaptation rather than accepted phylogenetic relationships. Fossorial lizards and mammals cluster together, whereas snakes are widely separated from these taxa and instead cluster with primitively aquatic vertebrates. This indicates that the eyes of snakes most closely resemble those of aquatic vertebrates, and suggests that the early evolution of snakes occurred in aquatic environments.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 469–482.     

The dynamic clonal genome and its adaptive potential

Populations of clonal organisms are often represented as being evolutionary inert with persistent genetic fidelity. The advent of molecular methods and the corresponding increased genetic resolution of clonal populations forces a reconsideration of this viewpoint. We review molecular data from viruses, prokaryotes and eukaryotes to support the argument that clones possess a highly dynamic and adaptive genome.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 193–208.     

Molecular and morphometric data demonstrate the presence of cryptic lineages among freshwater crabs (Decapoda: Potamonautidae: Potamonautes) from the Drakensberg Mountains, South Africa

The evolutionary importance of cryptic taxa is well documented, yet few studies have examined them with a view to conservation. In the present study, the significance of cryptic speciation in freshwater crabs is examined. Allozyme and 16S rRNA sequence data were used to explore the degree of population differentiation between mountain stream populations of two distinct freshwater crab species. Marked patterns of differentiation were evident among populations; those in close geographical proximity were characterized by the fixation of alternate alleles at certain loci, indicating that currently there is no gene flow among populations. Both allozyme and sequence data provide evidence for the recognition of at least five distinct evolutionary lineages with pronounced levels of genetic differentiation. Morphometric data failed to detect any distinct geographically intermediate population groupings. Our findings indicate the presence of five phylogeographical units, all worthy of conservation, three of which are evolutionarily significant.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78 , 129–147.     

The Cladocera (Crustacea: Branchiopoda) as a relict group

According to the fossil record and DNA data, the Cladocera is an ancient crustacean group. Recent revisions make their taxonomy amenable to zoogeographical analysis. A bipolar (antitropical) disjunct distribution of faunal complexes and taxa ( Daphnia , Daphniopsis , Pleuroxus , Tretocephala , etc.), the wide ranges of some species and narrow restriction of others, the presence of isolated populations and the concentration of endemics in the warm temperate – subtropical zone of both hemispheres are traits of cladoceran zoogeography. These enable us to compare them with better studied (both living and fossil) plants, invertebrates and vertebrates, and to analyse their faunal formation by the modern version of the concept of 'ejected relicts' instead of vicariance. This reveals the extant Cladocera as a relict group, whose taxa were widely distributed in the past. Tertiary climatic changes, primarily within the present tropical and boreal latitudes, resulted in mass extinction of their biotas, while the warm temperate – subtropical regions remained comparatively unchanged. Although most recent Cladocera have relict status, others such as the D. pulex and D. longispina species groups and the subgenus Eubosmina are evolutionary young and show recent speciation.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 109–124.     

Phylogeography and conservation genetics of endangered European Margaritiferidae (Bivalvia: Unionoidea)

Margaritifera margaritifera and M. auricularia are among the most endangered freshwater mussels in the world, and the only species of the genus found in Europe. Our genetic study explores allozymic variability (27 loci) and differentiation at the mitochondrial sequence level (partial COI and 16S rRNA gene sequences). The Spanish M. auricularia population showed genetic parameters of variation that were of the same order as those of other freshwater molluscs (though at the lower end of the range), probably permitting its potential recovery. The difference between this species and M. margaritifera was clearly established (ten diagnostic allozymic loci, Nei = 0.462, and mean nucleotide divergence around 9.4%). The M. margaritifera populations analysed showed a certain degree of population genetic structure (according to allozyme data) that was not, however, related to a geographical cline. Nevertheless, two mitochondrial lineages (albeit very closely related) were identified: a northern lineage extending from Ireland to the Kola Peninsula including the western Atlantic coast, and a second cluster distributed from Ireland to the Iberian Peninsula. The phylogenetic relationships between these two species and other related taxa were established. The putative M. m. durrovensis could be considered an 'ecophenotype'. Palaeobiogeographical scenarios are presented and indicate unexpected 'recent' gene flow between M. margaritifera populations that were theoretically isolated in the early Tertiary.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 235–252.