Blood-protein allele frequencies and phylogenetic relationships in Macaca: A review

Allele-frequency data have been assembled for 35 blood-protein loci in 17 of 19 recognized species of Macaca based on 29 published electrophoretic studies; studies of inbred captive colonies have been excluded. Data for 22 polymorphic loci are tabulated in detail for 43 geographic populations of these species. Calculated F_ST values provide a measure of intergroup genetic differentiation at various hierarchical levels—troop, locality, province, country or island, species, species group; polymorphism indices measure genetic variation. The greatest intraspecific genetic differentiation occurs at the level of island populations within species. The pattern of genetic variation among island populations appears to be relictual, suggesting that the reduced genetic variability of island populations of macaques is a result of postisolation genetic drift rather than founder effect. Interspecific relationships were investigated by means of a jackknifed Fitch-Margoliash algorithm, using Papio as outgroup. Phylogenetic inferences based on morphology and zoogeography. The reduced genetic variability that frequently characterizes insular macaque populations complicates phylogenetic interpretation of blood-protein evidence.     

Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements

Genus Macaca (Cercopithecidae: Papionini) is one of the most successful primate radiations. Despite previous studies on morphology and mitochondrial DNA analysis, a number of issues regarding the details of macaque evolution remain unsolved. Alu elements are a class of non-autonomous retroposons belonging to short interspersed elements that are specific to the primate lineage. Because retroposon insertions show very little homoplasy, and because the ancestral state (absence of the SINE) is known, Alu elements are useful genetic markers and have been utilized for analyzing primate phylogenentic relationships and human population genetic relationships. Using PCR display methodology, 298 new Alu insertions have been identified from ten species of macaques. Together with 60 loci reported previously, a total of 358 loci are used to infer the phylogenetic relationships of genus Macaca. With regard to earlier unresolved issues on the macaque evolution, the topology of our tree suggests that: 1) genus Macaca contains four monophyletic species groups; 2) within the Asian macaques, the silenus group diverged first, and members of the sinica and fascicularis groups share a common ancestor; 3) Macaca arctoides are classified in the sinica group. Our results provide a robust molecular phylogeny for genus Macaca with stronger statistical support than previous studies. The present study also illustrates that SINE-based approaches are a powerful tool in primate phylogenetic studies and can be used to successfully resolve evolutionary relationships between taxa at scales from the ordinal level to closely related species within one genus.     

ELECTROPHORETIC ENZYME ANALYSIS OF NORTH AMERICAN AND EASTERN ASIAN POPULATIONS OF AGASTACHE SECT. AGASTACHE (LABIATAE)

Agastache sect. Agastache consists of seven species in North America and one disjunct in eastern Asia. Starch-gel electrophoresis of enzymatic proteins was employed to assess genetic relationships among these species and to estimate the amount of genetic divergence between the North American and Asian populations. Species of the western United States appear to be better adapted for outcrossing than are the others and are much more genetically variable, with higher levels of heterozygosity per individual, more alleles per species, and higher percentages of polymorphic loci per population. Nonmetric multidimensional scaling of Nei's genetic distances among 32 populations partitioned the section into four discrete groups: 1) A. nepetoides (eastern North America), 2) A. scrophulariifolia and A. foeniculum (eastern and central North America), 3) the four species of the western United States (A. urticifolia, A. occidentalis, A. parvifolia and A. cusickii) and 4) A. rugosa (eastern Asia). Asian Agastache, separated from its American congeners for over twelve million years, differed from American populations at two of fifteen loci surveyed. Nei's genetic distances between Asian and North American populations ranged from 0.2877 to 0.6734.     

Radiation and phylogeography in the Japanese macaque, Macaca fuscata

The Japanese macaque (Macaca fuscata) presumably differentiated from eastern rhesus macaque (Macaca mulatta) populations during the Pleistocene and the two species are closely related. In order to analyse speciation and subspeciation events in the Japanese macaque and to describe historical and current relationships among their populations, we sequenced and analysed a fragment of 392bp of mitochondrial DNA (mtDNA) control region in 50 individuals belonging to six populations of Japanese macaque and compared these sequences with 89 eastern rhesus macaque control region sequences from GenBank/EMBL database. There were high genetic similarities between both species and only two positions were fixed within each species, which supports the inclusion of the Japanese macaque in a single species with eastern populations of rhesus macaques. Japanese macaque ancestors colonised Japan after the separation of the two species, estimated at between 0.31 and 0.88 million years ago (Mya). The star-like phylogeny, multimodal mismatch distribution, and lack of correlation between geographic and genetic distances are in accordance with a rapid dispersion of macaques throughout the archipelago after the arrival into Japan. The species shows low genetic variation within populations and high levels of genetic differentiation among populations with no mtDNA haplotype shared across populations. Genetic distances between Yakushima macaques (Macaca fuscata yakui) and any other population of Macaca fuscata fuscata subspecies are comparable to the distances between populations of Honshu, Awajishima, and Kyushu, not supporting the classification of Yakushima macaques as a different subspecies.     

Characterization of Gypsophila species and commercial hybrids with nuclear whole-genome and cytoplasmic molecular markers

The genus Gypsophila contains about 150 annual and perennial flowering plant species native to the temperate regions of Europe and Asia. Nowadays Gypsophila species are present worldwide as garden ornamental plants. Although Gypsophila is one of the most economically important ornamental crops, little is known about its genetic variability and the relationships among the different wild species, cultivars, and commercial hybrids. The aim of our work was to analyze genetic distances among 5 wild species and 13 commercial hybrids of Gypsophila with similar phenotypes but unknown origin. For this purpose, we have used amplified fragment length polymorphism, target region amplification polymorphism, and inter simple sequence repeat whole-genome markers and chloroplast simple sequence repeat (cpSSR), targeting chloroplast DNA. Nuclear markers were found to distinguish all the analyzed samples while cpSSR markers were found to discriminate the different wild species, but could not sufficiently separate the commercial hybrids. This notwithstanding, the data obtained allowed us to cluster the commercial hybrids into different sub-groups and to determine the relationships with the putative species of origin.     

Mitochondrial COI and 16sRNA Evidence for a Single Species Hypothesis of E. vitis,J. formosana and E. onukii in East Asia

Tea green leafhopper is one of the most damaging tea pests in main tea production regions of East Asia. For lack of recognized morphological characters, the dominant species of tea green leafhoppers in Mainland China, Taiwan and Japan have always been named as Empoasca vitis Göthe, Jacobiasca formosana Paoli and Empoasca onukii MATSUDA, respectively. Furthermore, nothing is known about the genetic relationships among them. In this study, we collected six populations from Mainland China, four populations from Japan and one population from Taiwan, and examined the genetic distances in the COI and 16sRNA regions of mtDNA among them. The results showed that the genetic distances based on single gene or the combined sequences among eleven leafhopper populations were 0.3–1.2%, which were all less than the species boundary of 2%. Moreover, there were at least two haplotypes shared by two distinct populations from different regions. The phylogenetic analysis based on single gene or combined sets also supported that tea green leafhoppers from Mainland China, Taiwan and Japan were closely related to each other, and there were at least two specimens from different regions clustered ahead of those from the same region. Therefore, we propose that the view of recognizing the dominant species of tea green leafhoppers in three adjacent tea production regions of East Asia as different species is unreliable or questionable and suggest that they are a single species.     

Four mutually incompatible Argentine ant supercolonies in Japan: inferring invasion history of introduced Argentine ants from their social structure

In recent years, highly invasive ant species successively invaded warm regions of Asia. In Japan, the Argentine ant, Linepithema humile, has become established in several coastal regions. This species forms unusual social organizations called supercolonies consisting of numerous mutually non-aggressive nests. We studied the behavioral relationships, similarity of cuticular hydrocarbon profiles (nestmate recognition cue), and genetic relationships among the introduced Argentine ant populations of Japan. The Japanese populations were divided into four behaviorally, chemically, and genetically distinct supercolonies, which may have derived from independent source populations. The result represents the recent trend of increasing invasions of invasive ants to Asia. The discontinuous distribution of one supercolony throughout most of the Japanese range suggests rapid expansion of the supercolony via human-mediated jump dispersal. Meanwhile, localization of the other three supercolonies in Kobe Port provides the first evidence for multiple invasions of distinct supercolonies into a base for international trade.     

Analysis of the genetic diversity and relationships among and within species of Hippophae (Elaeagnaceae) based on RAPD markers

RAPD markers were used to assess the genetic diversity and inter- and intra-specific relationships of the genus Hippophae L. and to study the correlation between genetic distances and geographic distances among populations of H. rhamnoides ssp. sinensis. The results analyzed by the percentage of polymorphic loci and Shannon information index indicated that a high level of genetic diversity existed both among and within species of the genus Hippophae. In the UPGMA dendrogram, the species or subspecies were clustered into two main groups but not strictly grouped according to sect. Hippophae and sect. Gyantsensis Lian. The multiple regression analysis and Mantel test both indicated a significant correlation between genetic distance and altitude distance among populations of H. rhamnoides ssp. sinensis, and the cluster analysis suggested that the genetic variation among populations of H. rhamnoides ssp. sinensis was linked to their monophyletic origin. Moreover, some degree of genetic differentiation was found among samples collected at different times.     

Ecology of malaria parasites infecting Southeast Asian macaques: evidence from cytochrome b sequences

Although malaria parasites infecting non‐human primates are important models for human malaria, little is known of the ecology of infection by these parasites in the wild. We extensively sequenced cytochrome b (cytb) of malaria parasites (Apicomplexa: Haemosporida) from free‐living southeast Asian monkeys Macaca nemestrina and Macaca fascicularis. The two most commonly observed taxa were Plasmodium inui and Hepatocystis sp., but certain other sequences did not cluster closely with any previously sequenced species. Most of the major clades of parasites were found in both Macaca species, and the two most commonly occurring parasite infected the two Macaca species at approximately equal levels. However, P. inui showed evidence of genetic differentiation between the populations infecting the two Macaca species, suggesting limited movement of this parasite among hosts. Moreover, coinfection with Plasmodium and Hepatocystis species occurred significantly less frequently than expected on the basis of the rates of infection with either taxon alone, suggesting the possibility of competitive exclusion. The results revealed unexpectedly complex communities of Plasmodium and Hepatocystis taxa infecting wild southeast Asian monkeys. Parasite taxa differed with respect to both the frequency of between‐host movement and their frequency of coinfection.     

Génétique des populations,spéciation et taxonomie chez les Babouins: II — Similitudes génétique comparées entre différentes espèces : Papio papio,P. anubis,P. cynocephalus et P. hamadryas basées sur les données du polymorphisme des enzymes erythrocytaires

The taxonomical status of the five Papio species is controversial. Certain authors consider them as geographical races of a single polytypic species. Natural populations of four species, Papio papio, P. anubis, P. cynocephalus and P. hamadryas, have been investigated for electrophoretical polymorphism of 10 intra-erythrocyte enzymes. It was found that 4 genes out of 14 studied loci exhibit genetic variability in the four Papio species, and that the same isozymes are concerned. The enzymatic variants have low allelic frequencies, and the levels of heterozygoty are consequently low. Although various formulae are utilised by various authors to measure the genetic distances between groups, the values obtained for the four studied species show the same order of magnitude as those obtained among species of the genus Macaca. Among the four Papio forms, Papio papio is very similar to P. anubis, and P. hamadryas appears as the most different from the others. The divergence is similar to that of subspecies of a polytypic species: in fact, no allele appears differentially fixed in any of these groups. The comparison with mean genetic distances evaluated among various mammalian species confirms that view. However, the genetic distances were obtained from mutant alleles showing low genic frequencies and our conclusion is inferred from a group of enzymes chosen empirically.     

Variation in coding exons of two electrophoretic alleles at the pigtail macaque carbonic anhydrase I locus as determined by direct,double-stranded sequencing of polymerase chain reaction (PCR) products

Two, electrophoretically distinct, forms of carbonic anhydrase I (CA Ia and CA Ib) are found at high polymorphic frequencies in red cells of natural populations of pigtail macaques,Macaca nemestrina, from southeast Asia. By use of the polymerase chain reaction, exons of the CA I gene were amplified from homozygous (a/a, b/b) and heterozygous (a/b) animals. Direct sequencing of the amplified DNA from four animals revealed differences between the a and the b electrophoretic alleles ranging from three to six nucleotides, and from one to three differences within each allele. These results indicate a greater genetic variability at the CA I locus in this macaque species than previously realized. We thank the personnel of the University of Washington, Regional Primate Research Center, Seattle, for sending us blood and tissue samples from pigtail macaques (supported by NIH Grant RR 00166). Our work was supported by NIH Grant GM 24681.     

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N _ST =0.751> G _ST =0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s F_S indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.     

<Emphasis Type="Italic">Macaca munzala</Emphasis>: A New Species from Western Arunachal Pradesh,Northeastern India<Superscript>*</Superscript>

Macaca, comprising 20 well-characterized species, represents the largest and one of the most ecologically and socially diverse of all the nonhuman primate genera. We report the discovery of a macaque that is new to science from the high altitudes of western Arunachal Pradesh, a biodiversity-rich state in northeastern India. We propose the scientific name Macaca munzala and the vernacular name Arunachal macaque for the species. It shares morphological characteristics independently with the Assamese macaque (Macaca assamensis) and with the Tibetan macaque M. thibetana; like them, it appears to belong to the sinica species-group of the genus. However, the species is distinctive in relative tail length, which is intermediate between those of Tibetan and Western Assamese macaques, the subspecies with which it is sympatric. It is also unique in its altitudinal distribution, occurring largely at altitudes between 2000 and 3500 m. We provide a morphological characterization of the species, report preliminary data on its field biology and discuss possible taxonomic identity in relation to the other closely-related species of Macaca.^*This paper is dedicated to Dr. A. J. T. Johnsingh for his immense contributions to the study and conservation of India’s wildlife and for being an inspiration to a whole generation of students.     

Ecogeographic segregation of macaque species

Sympatry in the genusMacaca is restricted to a heartland area in South Asia that is inhabited by eight species. All heartland species apparently are segregated either ecologically or geographically. Available evidence is compatible with the hypothesis that interspecific competition has been a major factor in the evolution of this pattern of ecogeographic segregation.     

A likelihood-based comparison of population histories in a parasitoid guild

Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and—using triplet alignments of intronic loci—quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.     

Nonhuman primate hybridization and the taxonomic status of Neanderthals

The present study examines the taxonomic status of Middle Paleolithic Neanderthals by comparing their observed minimum genetic divergence from Upper Paleolithic modern humans in Europe with that observed between macaque species from Sulawesi that are known to hybridize and fully intergrade in the wild. The genetic divergence, and differentiation between Neanderthals and Upper Paleolithic modern humans, as indicated by pairwise minimum genetic distances and F(ST) values calculated from the estimated minimum genetic relationship (R) matrix derived from craniometric data, are significantly greater than those observed both between hybridizing and noninterbreeding Sulawesi macaque species, suggesting that mate recognition and the possibility of gene flow between Neanderthals and Upper Paleolithic modern humans might have been greatly reduced. These results support a species-level taxonomic distinction for the Neanderthals as suggested by proponents of the replacement model. Furthermore, assumptions regarding the monophyletic origin of modern humans from outside Europe are likely valid.     

Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust

The migratory locust, Locusta migratoria, is the most widely distributed grasshopper species in the world. However, its global genetic structure and phylogeographic relationships have not been investigated. In this study, we explored the worldwide genetic structure and phylogeography of the locust populations based on the sequence information of 65 complete mitochondrial genomes and three mitochondrial genes of 263 individuals from 53 sampling sites. Although this locust can migrate over long distances, our results revealed high genetic differentiation among the geographic populations. The populations can be divided into two different lineages: the Northern lineage, which includes individuals from the temperate regions of the Eurasian continent, and the Southern lineage, which includes individuals from Africa, southern Europe, the Arabian region, India, southern China, South‐east Asia and Australia. An analysis of population genetic diversity indicated that the locust species originated from Africa. Ancestral populations likely separated into Northern and Southern lineages 895 000 years ago by vicariance events associated with Pleistocene glaciations. These two lineages evolved in allopatry and occupied their current distributions in the world via distinct southern and northern dispersal routes. Genetic differences, caused by the long‐term independent diversification of the two lineages, along with other factors, such as geographic barriers and temperature limitations, may play important roles in maintaining the present phylogeographic patterns. Our phylogeographic evidence challenged the long‐held view of multiple subspecies in the locust species and tentatively divided it into two subspecies, L. m. migratoria and L. m. migratorioides.     

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.     

Normal serum biochemical and hematological values of the Sulawesi macaques

Sulawesi macaque (SM) species are currently of interest to primatologists for genetic and behavioral studies world wide. However, there are no published reference hematological and serum biochemical profile values for several of the seven SM species. Twenty-five clinically healthy, outdoor housed, ketamine sedated Macaca tonkeana and Macaca maurus were serially sampled (two to four times) over a 16-month period (N = 68). Normal ranges were defined to include two standard deviations and 2.5–97.5 percentile. Significant differences in single sample date comparisons (P < 0.05) of species (serum Ca, MCHC), age (BUN, BUN/creatinine, alkaline phosphatase, phosphorus), gender (total protein, RBC, hemoglobin, HCT) and pregnancy (phosphorus and neutrophil count) groups were found. This normative data facilitates clinical evaluation of SM species and allows comparison to other macaque species.