Climate Change Estimates Surpass Rates of Climatic Niche Evolution in Primates

International Journal of Primatology - Primates might be particularly vulnerable to experiencing adverse effects from climate change, given their level of exposure, sensitivity to climatic...     

The Evolution of Cultural Diversity: A Phylogenetic Approach

The Evolution of Cultural Diversity:. Phylogenetic Approach . Ruth Mace, Clare J. Holden, and Stephen Shennan, eds. Oxford, U.K.: Cavendish Publishing, 2005. 291 pp.     

Interspecific Competition and Niche Separation in Primates: A Global Analysis

Primates are an extraordinarily well-known tropical forest, mammalian taxon. We investigated potential modes of niche separation in primates by identifying sympatric species with putatively similar niche characteristics and assessing potential competition using data gleaned from an extensive literature review. We defined competing species-pairs as (a) sympatric species in which (b) the body mass of the larger species was within 30 percent of the smaller species' mass and (c) the species had the same category of diet. A sample of 43 well-studied forests (7–20 per continent) provided 673 pairs of sympatric primate species. Of these, 45 pairs (7%) are potential competitors by our definition. Africa has the largest number of competing pairs (17 pairs), while Asia might have the highest percentage of competitors in each forest site (17%). Niche separation was investigated for each pair by examining them for each of eight possible modes of separation: detailed differences in diets (28% of potential competitors), use of different heights in the forest (25%), use of different types of forest (14%), use of different locations within the forest (11%), use of support branches of different diameters (7%), different ranging behavior (6%), different techniques of prey capture (4%), and differential timing of activity (4%). The use of different heights in the forest is the dominant form of potential separation in Africa (31% of competing species-pairs) and Asia (38%), while detailed differences in diet appears to be the primary mode of niche separation in the Americas (26%) and Madagascar (32%).     

Phylogenetic relationships among the Malagasy lemuriforms (Primates: Strepsirrhini) as indicated by mitochondrial sequence data from the 12S rRNA gene

Numerous phylogenetic hypotheses have been advanced for the Malagasy lemuriform radiation, drawing on data from morphology, physiology, behaviour and molecular genetics. Almost all possible relationships have been proposed and most nodes have been contested. We present a phylogenetic analysis, using several analytical methods, of a partial sequence from the 12s rRNA mitochondrial gene. This gene codes for the small ribosomal subunit, and functional constraints require that the secondary structure of the molecule is strongly conserved, which in inturn exerts constraints on the primary sequence structure. Although previous studies have suggested a very wide range of phylogenetic applicability for this molecule, our results indicate that it is most useful in strepsirrhine primates for estimating relationships among genera within families and among relatively recently diverged families (mean sequence divergence about 11%). Relationships among families separated by larger genetic distances (>12% divergence; e.g. Cheirogaleidae, Daubentoniidae, Megaladapidae) are difficult to resolve consistently. Our data show strong support for an Indridae-Lemuridae sister group and for monophyly of the Lemuridae with Varecia as the sister to all other lemurids. They also support, albeit less strongly, sister group relationships between Lemur and Hapalemur within the Lemuridae and between PmpLthecus and Avahi in the Indridae.     

Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.     

Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA

The family Lemuridae includes four genera: Eulemur, Hapalemur, Lemur,Varecia. Taxonomy and phylogenetic relationships between L. catta, Eulemur and Hapalemur, and of Varecia to these other lemurids, continue to be hotly debated. Nodal relationships among the five Eulemur species also remain contentious. A mitochondrial DNA sequence dataset from the ND 3, ND 4 L, ND 4 genes and five tRNAs (Gly, Arg, His, Ser, Leu) was generated to try to clarify phylogenetic relationships w ithin the Lemuridae. Samples (n=39) from all ten lemurid species were collected and analysed. Three Daubentonia madagascariensis were included as outgroup taxa. The approximately 2400 bp sequences were analysed using maximum parsimony, neighbor-joining and maximum likelihood methods. The results support monophyly of Eulemur, a basal divergence of Varecia, and a sister-group relationship for Lemur/Hapalemur. Based on tree topology, bootstrap values, and pairwise distance comparisons, we conclude thatVarecia and Eulemur both represent distinct genera separate from L. catta. H. griseus andH. aureus form a clade with strong support, but the sequence data do not permit robust resolution of the trichotomy involving H. simus, H. aureus/H. griseus and L. catta. Within Eulemur there is strong support for a clade containing E. fulvus, E. mongoz and E. rubriventer. However, analyses failed to clearly resolve relationships among those three species or with the more distantly related E. coronatus and E. macaco. Our sequencing data support the current subspecific status of E.m. macaco and E.m. flavifrons, and that of V.v. variegata and V.v. rubra. However, tree topology and relatively large genetic distances among individual V.v. variegata indicate that there may be more phylogenetic structure within this taxon than is indicated by current taxonomy.     

Assessment of the Diversity of African Primates

This account of the systematics of African primates is the consensus view of a group of authors who attended the Workshop of the IUCN/SSC Primate Specialist Group held at Orlando, Florida, in February 2000. We list all species and subspecies that we consider to be valid, together with a selected synonymy for all names that have been controversial in recent years or that have been considered to be valid by other authors in recent publications. For genera, species-groups or species, we tabulate and discuss different published systematic interpretations, with emphasis on more recent publications. We explain why we have adopted our taxonomic treatment and give particular attention to cases where more research is urgently required and in which systematic changes are most likely to be made. For all taxa, from suborder to subspecies, we provide English names.     

Scaling of Sexual Dimorphism in Body Mass: A Phylogenetic Analysis of Rensch's Rule in Primates

We examined the relationship between body mass dimorphism, measured as the natural logarithm of the male/female ratio, and body mass, defined as ln (female mass), with interspecific allometry, phylogenetically independent contrasts, and phylogenetic autocorrelation in 105 primate species. We repeated the analyses for Strepsirhini (N = 23), Haplorhini (N = 82), Platyrrhinii (N = 32), and Catarrhini (N = 47). With independent contrasts, there is statistically significant (p < .05) positive allometry in Primates in general, Haplorhini, and Catarrhini, but not in Strepsirhini or Platyrrhini. The steepest slope (0.134) is for Catarrhini. Results differed when we conducted analyses with traditional interspecific allometry. For example, not only was the Catarrhini slope not statistically significant but also the magnitude of the slope was shallower than that of all other groups, except Strepsirhini. The results indicate that phylogenetic effects influence the scaling of sexual size dimorphism, and that the statistical method used has a large impact on the interpretation of this biological relationship. We discuss issues involved in applying these statistical methods in detail.     

Central Lateral Line and Auditory Pathways: A Phylogenetic Perspective

The phylogenetic origins of the lateral line electrosensory,lateral line mechanosensory, and auditory components of theoctavolateralis system are unknown but each of these sensorymodalities appears to have evolved early in vertebrate history.The octavolateralis terminal field occupies a large area ofthe dorsolateral wall of the medulla and among agnathids, cartilaginousfishes, non-teleost bony fishes and, with modifications, urodeles,consists of a dorsal electrosensory nucleus, a medial mechanosensorynucleus and a ventral octaval nuclear complex. This arrangementof medullary octavolateral nuclei, which differs from that ofnon-electroreceptive and electroreceptive teleosts, is consideredthe primitive plan and is retained in that phyletic line leadingto tetrapods. Separate and parallel pathways are known, in elasmobranchsand a few teleosts, to ascend from each medullary lateral linecenter to the midbrain and presumably from midbrain to telencephaliclevels via thalamic relays. There is no evidence, with the lossof lateral line senses among some amphibians and all amniotes,that the central neural pathways and nuclei are retained andused to process information from other sensory modalities. Theanatomy of the central auditory system of fishes is unknownbut is required for an understanding of whether auditory nucleiand pathways are retained during the fishamphibian transition,or whether new ones arise, to process information from independentlyevolved peripheral receptors.     

On the Diversity of the Laccase Gene: A Phylogenetic Perspective from Botryosphaeria rhodina (Ascomycota: Fungi) and Other Related Taxa

The present study is the first describing the sequencing of a fragment of the copper-oxidase domain of a laccase gene in the family Botryosphaeriaceae. The aim of this work was to assess the degree of genetic and evolutionary relationships of a laccase gene from Botryosphaeria rhodina MAMB-05 with other ascomycete and basidiomycete laccase genes. The 193-amino acid sequences of the copper-oxidase domain from several different fungi, insects, a plant, and a bacterial species were retrieved from GenBank and aligned. Phylogenetic analyses were performed using neighbor-joining, maximum parsimony, and Bayesian inference methods. The organisms studied clustered into five gene clades: fungi (ascomycetes and basidiomycetes), insects, plants, and bacteria. Also, the topologies showed that fungal laccases of the ascomycetes and basidiomycetes are clearly separated into two distinct clusters. This evidence indicated that B. rhodina MAMB-05 and other closely related ascomycetes are a new biological resource given the biotechnological potential of their laccase genes.     

Trophic Niche in a Raptor Species: The Relationship between Diet Diversity,Habitat Diversity and Territory Quality

Recent research reports that many populations of species showing a wide trophic niche (generalists) are made up of both generalist individuals and individuals with a narrow trophic niche (specialists), suggesting trophic specializations at an individual level. If true, foraging strategies should be associated with individual quality and fitness. Optimal foraging theory predicts that individuals will select the most favourable habitats for feeding. In addition, the “landscape heterogeneity hypothesis” predicts a higher number of species in more diverse landscapes. Thus, it can be predicted that individuals with a wider realized trophic niche should have foraging territories with greater habitat diversity, suggesting that foraging strategies, territory quality and habitat diversity are inter-correlated. This was tested for a population of common kestrels Falco tinnunculus. Diet diversity, territory occupancy (as a measure of territory quality) and habitat diversity of territories were measured over an 8-year period. Our results show that: 1) territory quality was quadratically correlated with habitat diversity, with the best territories being the least and most diverse; 2) diet diversity was not correlated with territory quality; and 3) diet diversity was negatively correlated with landscape heterogeneity. Our study suggests that niche generalist foraging strategies are based on an active search for different prey species within or between habitats rather than on the selection of territories with high habitat diversity.     

Patterns of Phylogenetic Diversity of Subtropical Rainforest of the Great Sandy Region,Australia Indicate Long Term Climatic Refugia

Australia’s Great Sandy Region is of international significance containing two World Heritage areas and patches of rainforest growing on white sand. Previous broad-scale analysis found the Great Sandy biogeographic subregion contained a significantly more phylogenetically even subset of species than expected by chance contrasting with rainforest on white sand in Peru. This study aimed to test the patterns of rainforest diversity and relatedness at a finer scale and to investigate why we may find different patterns of phylogenetic evenness compared with rainforests on white sands in other parts of the world. This study focussed on rainforest sites within the Great Sandy and surrounding areas in South East Queensland (SEQ), Australia. We undertook field collections, expanded our three-marker DNA barcode library of SEQ rainforest plants and updated the phylogeny to 95% of the SEQ rainforest flora. We sampled species composition of rainforest in fixed area plots from 100 sites. We calculated phylogenetic diversity (PD) measures as well as species richness (SR) for each rainforest community. These combined with site variables such as geology, were used to evaluate patterns and relatedness. We found that many rainforest communities in the Great Sandy area were significantly phylogenetically even at the individual site level consistent with a broader subregion analysis. Sites from adjacent areas were either not significant or were significantly phylogenetically clustered. Some results in the neighbouring areas were consistent with historic range expansions. In contrast with expectations, sites located on the oldest substrates had significantly lower phylogenetic diversity (PD). Fraser Island was once connected to mainland Australia, our results are consistent with a region geologically old enough to have continuously supported rainforest in refugia. The interface of tropical and temperate floras in part also explains the significant phylogenetic evenness and higher than expected phylogenetic diversity.     

系统发育多样性与系统发育结构在岛屿植物群落保护中的意义——以蜈支洲岛为例

为探讨系统发育多样性和系统发育结构在岛屿植物群落保护决策制定中的作用,以海南三亚蜈支洲岛被子植物群系为例,分析物种丰富度和系统发育多样性的相关性。结果表明,蜈支洲岛植被可分为10种群系类型,22个样方的物种丰富度与系统发育多样性呈显著正相关,但系统发育多样性与物种丰富度对植物多样性保护优先顺序的指示有差异。森林群系的物种丰富度和系统发育多样性普遍高于灌木和草本群系,4个森林群系样方表现为系统发育结构发散,3个森林群系样方表现为系统发育结构聚集。灌木群系中露兜树(Pandanus tectorius)灌丛和草海桐(Scaevola sericea)灌丛系统发育多样性较高,草本群系中厚藤(Vitex trifolia)灌草丛系统发育多样性较高,灌木和草本群系大多倾向于系统发育结构聚集。距海或人类活动区较近的群系可能受环境过滤的作用,而远离海和人类活动区的群系主要受竞争排斥作用影响。因此,在岛屿植物多样性保护策略制定中应当综合考虑物种和系统发育维度,以及环境、演替阶段及用岛方式等因素的影响。     

Macroecological Patterns of Climatic Niche Breadth Variation in Lacertid Lizards

Measuring climatic niche position and breadth may help to determine where species can occur over space and time. Using GIS-based and phylogenetic comparative methods, we investigated global patterns of variation in climatic niche breadth in lacertid lizards to test the following three hypotheses about climatic niche widths. First, does a species' temperature or precipitation niche breadth relate to its temperature or precipitation niche position(the mean value of annual mean temperature or annual precipitation across sampled localities in the range of each species)? Second, are there trade-offs between a species' temperature niche breadth and precipitation niche breadth? Third, does a species' temperature or precipitation niche breadth relate to altitude or latitude? We expect that:(1) species distributed in cold regions are specialized for low-temperature environments(i.e. narrow niche breadth center around low temperatures);(2) a negative relationship between species niche breadth on temperature and precipitation axes according to the tradeoff hypothesis(i.e. species that tolerate a broad range of precipitation regimes cannot also tolerate a broad range of temperatures);(3) precipitation niche breadth decreases with altitude or latitude, whereas temperature climatic niche breadth increases with altitude or latitude. Based on the analytical results we found that:(1) temperature niche breadth and position are negatively related, while precipitation niche breadth and position are positively related;(2) there is no trade-off between temperature and precipitation niche breadths; and (3) temperature niche breadth and latitude/altitude are positively related, but precipitation niche breadth and latitude/altitude are not significantly related. Our results show many similarities with previous studies on climatic niche widths reported for amphibians and lizards, which provide further evidence that such macroecological patterns of variation in climatic niche breadths may be widespread.