Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within-species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).

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Niche conservatism as an emerging principle in ecology and conservation biology.

Much as Rachel Carson's \"Silent Spring\" was a call to action against the pesticides that were devastating bird populations, Charles S. Elton's classic \"The Ecology of Invasions by Animals and Plants\" sounded an early warning about an environmental catastrophe that has become all too familiar today-the invasion of nonnative species. From kudzu to zebra mussels to Asian long-horned beetles, nonnative species are colonizing new habitats around the world at an alarming rate thanks to accidental and intentional human intervention. One of the leading causes of extinctions of native animals and plants, invasive species also wreak severe economic havoc, causing $79 billion worth of damage in the United States alone. Elton explains the devastating effects that invasive species can have on local ecosystems in clear, concise language and with numerous examples. The first book on invasion biology, and still the most cited, Elton's masterpiece provides an accessible, engaging introduction to one of the most important environmental crises of our time. Charles S. Elton was one of the founders of ecology, who also established and led Oxford University's Bureau of Animal Population. His work has influenced generations of ecologists and zoologists, and his publications remain central to the literature in modern biology. \"History has caught up with Charles Elton's foresight, and \"The Ecology of Invasions\" can now be seen as one of the central scientific books of our century.\"-David Quammen, from the Foreword to \"Killer Algae: The True Tale of a Biological Invasion\

The Ecology of Invasions by Animals and Plants

Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).

https://www.ruor.uottawa.ca/bitstream/10393/31435/1/Mol%20Biol%20Evol-2013-Xia-1720-8.pdf

DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the “bush at the top of the tree” that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the “Second Age of Fishes.”

https://www.pnas.org/content/pnas/109/34/13698.full.pdf

Resolution of ray-finned fish phylogeny and timing of diversification

We synthesized information on freshwater fish biodiversity in the Yangtze River basin We documented 361 species and subspecies that had been recorded and described from the basin Of these, 177 species are endemic The basin is usually divided into three parts, ie the upper reaches, the middle reaches and the lower reaches This study indicated that the ‘three reaches’ approach was not supported by fish distribution patterns Hydrological alterations are perhaps the largest threat to fish biodiversity in the basin Fishes in the upper reaches will be seriously affected by the construction of the Three Gorges Dam and other dams, and action should be taken for priority conservation The most immediate restoration need is reconnection of the Yangtze River with its lakes The cluster of lakes in the Central Yangtze should be protected to maintain habitats for spawning, feeding and migration of migratory fishes Our study indicates a need to identify areas of high fish biodiversity and to select nature reserves to mitigate the loss of fish biodiversity in the Yangtze River basin

Freshwater fish biodiversity in the Yangtze River basin of China: patterns, threats and conservation

We studied frog biodiversity along an elevational gradient in the Hengduan Mountains, China. Endemic and non-endemic elevational diversity patterns were examined individually. Competing hypotheses were also tested for these patterns. Species richness of total frogs, endemics and non-endemics peaked at mid-elevations. The peak in endemic species richness was at higher elevations than the maxima of total species richness. Endemic species richness followed the mid-domain model predictions, and showed a nonlinear relationship with temperature. Water and energy were the most important variables in explaining elevational patterns of non-endemic species richness. A suite of interacting climatic and geometric factors best explained total species richness patterns along the elevational gradient. We suggest that the mid-domain effect was an important factor to explain elevational richness patterns, especially in regions with high endemism.

Elevational patterns of frog species richness and endemic richness in the Hengduan Mountains, China: geometric constraints, area and climate effects

Aim We studied elevational species richness patterns of Schizothorax fishes and identified the roles of ecological and evolutionary factors in shaping the patterns of elevational diversity.



Location  The Tibetan Plateau and its adjacent regions.



Methods  We assembled distribution and altitude data for all Schizothorax species using the literature. We merged ecological and evolutionary approaches to test the relationships between species richness and ecological factors (climate, area, the mid-domain effect) or evolutionary factors (diversification rates and time of colonization).



Results  We found that species richness of Schizothorax fishes peaked at mid-elevations. Rainfall, area, the mid-domain effect and diversification rate were weak predictors of the richness pattern. Temperature showed a nonlinear relationship with species richness. Temperature and time of colonization were the most important variables in explaining the elevational diversity pattern.



Main conclusion  Our findings indicate that the time-for-speciation effect and niche conservatism play important roles in variation of species richness.

Climate and history explain the species richness peak at mid‐elevation for Schizothorax fishes (Cypriniformes: Cyprinidae) distributed in the Tibetan Plateau and its adjacent regions

Aim To document patterns in diversity, altitudinal range and body size of freshwater fishes along an elevational gradient in the Yangtze River basin.

Location  The Yangtze River basin, China.

Methods  We used published data to compile the distribution, altitudinal range and body size of freshwater fishes. Correlation, regression, clustering and graphical analyses were used to explore patterns in diversity, altitudinal range and body size of freshwater fishes in 100-m elevation zones from 0 to 5200 m.

Results  Species richness patterns across the elevational gradient for total, non-endemic and endemic fishes were different. The ratio of endemics to total richness peaked at mid elevation. Land area on a 500-m interval scale explained a significant amount of the variation in species richness. Species density displayed two peaks at mid-elevation zones. The cluster analysis revealed five distinct assemblages across the elevation gradient. The relationship between elevational range size and the midpoint of the elevational range revealed a triangular distribution. The frequency distribution of log maximum standard length data displayed an atypical right-skewed pattern. Intermediate body sizes occurred across the greatest range of elevation while small and large body sizes possessed only small elevational amplitudes. The size-elevation relationship between the two major families revealed a very strong pattern of body size constraint among the Cobitidae with no corresponding elevational constraint and a lot of body size and elevational diversification among the Cyprinidae.

Main conclusion  The data failed to support either Rapoport's rule or Bergmann's rule.

http://wetland.ihb.cas.cn/zgsdyj/cmd/201409/P020140926561115492522.pdf

Patterns of diversity, altitudinal range and body size among freshwater fishes in the Yangtze River basin, China

The structure and temporal variations of the fish community in salt marshes of Chinese estuaries are poorly understood. Fish utilization of a salt marsh intertidal creek in the Yangtze River estuary was studied based on quarterly sampling surveys in July and November, 2004, and February and May, 2005. Fishes were collected by consecutive day and night samplings using fyke nets during the ebbing spring tides. A total of 25,010 individuals were caught during the study. 17 families and 33 species were documented, and the most species-rich family was Gobiidae. Three species, Synechogobius ommaturus, Chelon haematocheilus and Lateolabrax maculatus together comprised 95.65% of the total catch, which were also the most important commercial fishery species in the Yangtze River estuary. The fish community was dominated by juvenile individuals of estuarine resident species. Time of year significantly affected fish use of salt marshes, but no significant effects of diel periodicity on the fish community were found except for fish sampling in July. These findings indicate that salt marshes in the Yangtze River estuary may play important nursery roles for fish community.

Cuizhang Fu

Papers

Freshwater fish biodiversity in the Yangtze River basin of China: patterns, threats and conservation

Elevational patterns of frog species richness and endemic richness in the Hengduan Mountains, China: geometric constraints, area and climate effects

Climate and history explain the species richness peak at mid‐elevation for Schizothorax fishes (Cypriniformes: Cyprinidae) distributed in the Tibetan Plateau and its adjacent regions

Patterns of diversity, altitudinal range and body size among freshwater fishes in the Yangtze River basin, China

Fish utilization of a salt marsh intertidal creek in the Yangtze River estuary, China