Single Widespread Species Research Articles

Population distribution models: species distributions are better modeled using biologically relevant data partitions.

BackgroundPredicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions.ResultsDespite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit.ConclusionsBecause the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications.

Responses to historical climate change identify contemporary threats to diversity in Dodecatheon.

Anthropogenic climate change may threaten many species with extinction. However, species at risk today survived global climate change in recent geological history. Describing how habitat tracking and adaptation allowed species to survive warming since the end of the Pleistocene can indicate the relative importance of dispersal and natural selection during climate change. By taking this historical perspective, we can identify how contemporary climate change could interfere with these mechanisms and threaten the most vulnerable species. We focused on a group of closely related plant species in the genus Dodecatheon (Primulaceae) in eastern North America. Two rare species (Dodecatheon amethystinum and Dodecatheon frenchii) that are endemic to patchy cool cliffs may be glacial relicts whose ranges constricted following the last glacial maximum. Alternatively, these species may be extreme ecotypes of a single widespread species (Dodecatheon meadia) that quickly adapted to microclimatic differences among habitats. We test support for these alternative scenarios by combining ecophysiological and population genetic data at a regional scale. An important ecophysiological trait distinguishes rare species from D. meadia, but only a few northern populations of D. amethystinum are genetically distinctive. These relict populations indicate that habitat tracking did occur with historical climate change. However, relatively stronger evidence for isolation by distance and admixture suggests that local adaptation and genetic introgression have been at least as important. The complex response of Dodecatheon to historical climate change suggests that contemporary conservation efforts should accommodate evolutionary processes, in some cases by restoring genetic connectivity between ecologically differentiated populations.

Biogeography and diversification of hermit spiders on Indian Ocean islands (Nephilidae: Nephilengys)

The origin of the terrestrial biota of Madagascar and, especially, the smaller island chains of the western Indian Ocean is relatively poorly understood. Madagascar represents a mixture of Gondwanan vicariant lineages and more recent colonizers arriving via Cenozoic dispersal, mostly from Africa. Dispersal must explain the biota of the smaller islands such as the Comoros and the chain of Mascarene islands, but relatively few studies have pinpointed the source of colonizers, which may include mainland Africa, Asia, Australasia, and Madagascar. The pantropical hermit spiders (genus Nephilengys) seem to have colonized the Indian Ocean island arc stretching from Comoros through Madagascar and onto Mascarenes, and thus offer one opportunity to reveal biogeographical patterns in the Indian Ocean. We test alternative hypotheses on the colonization route of Nephilengys spiders in the Indian Ocean and simultaneously test the current taxonomical hypothesis using genetic and morphological data. We used mitochondrial (COI) and nuclear (ITS2) markers to examine Nephilengys phylogenetic structure with samples from Africa, southeast Asia, and the Indian Ocean islands of Madagascar, Mayotte, Réunion and Mauritius. We used Bayesian and parsimony methods to reconstruct phylogenies and haplotype networks, and calculated genetic distances and fixation indices. Our results suggest an African origin of Madagascar Nephilengys via Cenozoic dispersal, and subsequent colonization of the Mascarene islands from Madagascar. We find strong evidence of gene flow across Madagascar and through the neighboring islands north of it, while phylogenetic trees, haplotype networks, and fixation indices all reveal genetically isolated and divergent lineages on Mauritius and Réunion, consistent with female color morphs. These results, and the discovery of the first males from Réunion and Mauritius, in turn falsify the existing taxonomic hypothesis of a single widespread species, Nephilengys borbonica, throughout the archipelago. Instead, we diagnose three Nephilengys species: Nephilengys livida ( Vinson, 1863) from Madagascar and Comoros, N. borbonica ( Vinson, 1863) from Réunion, and Nephilengys dodo new species from Mauritius. Nephilengys followed a colonization route to Madagascar from Africa, and on through to the Mascarenes, where it speciated on isolated islands. The related golden orb-weaving spiders, genus Nephila, have followed the same colonization route, but Nephila shows shallower divergencies, implying recent colonization, or a moderate level of gene flow across the archipelago preventing speciation. Unlike their synanthropic congeners, N. borbonica and N. dodo are confined to pristine island forests and their discovery calls for evaluation of their conservation status.

Phylogeographic analysis and environmental niche modeling of the plain-bellied watersnake ( Nerodia erythrogaster) reveals low levels of genetic and ecological differentiation

Species that exhibit geographically defined phenotypic variation traditionally have been divided into subspecies. Subspecies based on phenotypic features may not comprise monophyletic groups due to selection, gene flow, and/or convergent evolution. In many taxonomic groups the number of species once designated as widespread is dwindling rapidly, and many workers reject the concept of subspecies altogether. We tested whether currently recognized subspecies in the plain-bellied watersnake Nerodia erythrogaster are concordant with relationships based on mitochondrial markers, and whether it represents a single widespread species. The range of this taxon spans multiple potential biogeographic barriers (especially the Mississippi and Apalachicola Rivers) that correspond with lineage breaks in many species, including other snakes. We sequenced three mitochondrial genes (NADH-II, Cyt- b, Cox-I) from 156 geo-referenced specimens and developed ecological niche models using Maxent and spatially explicit climate data to examine historical and ecological factors affecting variation in N. erythrogaster across its range. Overall, we found little support for the recognized subspecies as either independent evolutionary lineages or geographically circumscribed units and conclude that although some genetic and niche differentiation has occurred, most populations assigned to N. erythrogaster appear to represent a single, widespread species. However, additional sampling and application of nuclear markers are necessary to clarify the status of the easternmost populations.

Systematics of a widespread Southeast Asian frog,Rana chalconota(Amphibia: Anura: Ranidae)

The abundant Sundaland forest frog, Rana chalconota, has long been considered a single widespread species, although some authors have recommended its division into regional subspecies. The discovery of co-occurring pairs of morphologically distinct populations in three widely separated parts of the range led to a morphological and molecular analysis of populations from all parts of the known range. The results suggest that R. chalconota consists of at least seven species from Thailand through Borneo and Java. Existing names are applied to three of these species, R. chalconota (Schlegel), R. raniceps (Peters) and R. labialis Boulenger. We describe four others as new species and suggest the existence of one or two additional, unnamed species. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155, 123–147.

Morphological and chromosomal taxonomic assessment of Sylvilagus brasiliensis gabbi (Leporidae)

The cottontail rabbit species, Sylvilagus brasiliensis, is currently understood to be constituted by 18 subspecies ranging from east central Mexico to northern Argentina, and from sea level to at least 4800 m in altitude. This hypothesis of a single widespread polytypic species remains to be critically tested. In other species groups of Sylvilagus from other geographic areas, the use of chromosomal information has been important in delineating taxonomic boundaries. To date, however, no chromosomal data are available for Sylvilagus south of Mexico. Here we report the chromosomal complement of two individuals (a male and a female) putatively ascribed to Sylvilagus brasiliensis on the basis of morphological characters and collected from southern Península del Azuero in Panama. The diploid number (2n) of these two individuals was 38 and the fundamental number (autosomal arms, aFN) was 72. Karyotypes of S. brasiliensis from southern Mexico have reported two chromosomal forms: 2n=36, FN=68 and 2n=40, FN=76. We complement the chromosomal data with a morphological examination of the Panama specimens and of holotype materials pertinent to the taxonomic identity of Mesoamerican taxa of Sylvilagus. These findings, in association with others regarding the phylogenetic relationships of Sylvilagus from the Neotropics, reinforce the idea that the current taxonomic treatment of the species merits critical scrutiny. In particular, we excise Sylvilagus gabbi from subspecific synonymy with S. brasiliensis and remove the subspecies truei from brasiliensis to gabbi.

Cryptic sex and many-to-one coevolution in the fungus-growing ant symbiosis.

The fungus-growing ants have long provided a spectacular example of coevolutionary integration. Their ecological success is thought to depend largely on the evolutionary alignment of reproductive interests between ants and fungi after vertical transmission and the ancient suppression of fungal sexuality. In the present study we test these assumptions and provide the first evidence of recombination in attine cultivars, contradicting widely held perceptions of obligate clonality. In addition, we document long-distance horizontal transmission of symbionts between leaf-cutter ant species on mainland Central America and South America and those endemic to Cuba, suggesting both lack of pairwise coevolutionary specificity in ant/cultivar interactions and dispersal of symbionts independent of their ant hosts. The coevolution between leaf-cutters and their fungal symbionts is thus not reciprocally pairwise. Rather, a single widespread and sexual fungal symbiont species is engaged in multiple interactions with divergent ant lineages. Strict fungal clonality and vertical transmission evidently have not played a critical role in the long-term evolutionary or ecological success of this well known mutualism.

GEOGRAPHIC VARIATION IN THE MORPHOLOGY OF CROTALUS HORRIDUS (SERPENTES: VIPERIDAE)

The timber rattlesnake (Crotalus horridus) occurs in discontinuous populations across the eastern and central United States. The species exhibits high levels of polymorphism in morphological traits, especially in coloration and pattern. Previous studies recognized either distinct northern and southern subspecies or three regional morphs (northern, southern, and western), but the conflicting data sets and limited geographic sampling of previous studies have left the relationships among those regional variants unclear. In this study, univariate and multivariate statistics, analyzed in conjunction with a geographic information system, were used to examine geographic variation in 36 morphological characters recorded from 2420 specimens of C. horridus across its range.Univariate analyses detected substantial geographic variation in all meristic characters. Scutellation exhibited a general north–south pattern of variation, and most scale counts averaged higher in southern regions. Pattern characters differentiated the northeastern, central-eastern, and north-central regions from the southern and western regions. Coloration displayed a pattern of strong clinal variation among three broad areas consisting of the combined northeastern, central-eastern, and southern Appalachian regions, the northwestern regions, and the southern regions. Morphometric characters exhibited a general north–south pattern of geographic variation, with larger head and body sizes in southern regions. Sexual dimorphism was strong in ventral and subcaudal scales, and weak to moderate in band length and band spacing.Principal component analysis indicated that band length was the most important variable for characterizing geographic variation. The northeastern regions remained moderately distinct in all multivariate cluster analyses. The northwestern regions appeared very distinct in most cluster analyses for females. However, the clusters in all models showed extensive geographic overlap. Maps of the clusters revealed two north–south patterns of clinal variation across the northeastern, northwestern, and southern regions. The discordant patterns of variation among individual characters, overlapping patterns of coloration, and extensive overlap among the multivariate clusters collectively indicate that the putative zones of intergradation among recognized subpopulations of C. horridus are much broader than previously thought. Furthermore, because the general patterns of geographic variation are strongly clinal, our results support the conclusion that C. horridus is a single widespread species with variation too extensive and complex to be reflected by formal subspecific designations.

Phylogeography of colour polymorphism in the coral reef fish Pseudochromis fuscus, from Papua New Guinea and the Great Barrier Reef

Body colour has played a significant role in the evolution of coral reef fishes, but the phylogenetic level at which colour variation is expressed and the evolutionary processes driving the development and persistence of different colour patterns are often poorly understood. The aim of this study was to examine the genetic relationships between multiple colour morphs of Pseudochromis fuscus (family Pseudochromidae), both within and among geographic locations. Pseudochromis fuscus is currently described as a single species, but exhibits at least six discrete colour morphs throughout its range. In this study, P. fuscus from Papua New Guinea (PNG) and the Great Barrier Reef (GBR), Australia, formed three genetically distinct clades based on mitochondrial DNA (control region) sequence data: (1) yellow and brown morphs from the GBR and southern PNG, as well as an orange morph from southern PNG; (2) a pink morph from southern PNG; and (3) all three morphs (pink, orange and grey) found in Kimbe Bay, northern PNG. The three groups showed deep levels of divergence (d=14.6–25.4%), suggesting that P. fuscus is a complex of polychromatic species, rather than a single widespread species with many different colour morphs. Population genetic analyses indicate that the three clades have experienced unique evolutionary histories, possibly from differential effects of sea level fluctuations, barriers to gene flow and historical biogeography.

Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex

Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.

Geographic patterns of genetic diversity in subterranean amphipods of the Pilbara, Western Australia

Twenty-six species of subterranean amphipods have been described from the Pilbara, Western Australia, based on variation in morphological characters. Many are known only from single bores. The Pilbara is rich in iron ore, and thus, an understanding of species’ diversity and their distribution is necessary both to manage resources and to conserve fauna. A previous allozyme study of nine bores in a single catchment in the Pilbara found low levels of genetic differentiation among individuals, but the diversity was not associated with single bores. The area studied appeared to contain a single widespread species common to all nine bores, in sympatry with a second, rare species, represented by a single specimen. The present study analysed allozymic variation in amphipods from 26 bores in four additional catchments in the Pilbara, to test the generality of these findings. At each site, samples with similar allelic arrays were found in multiple bores, in sympatry with rare divergent genotypes. Geological complexity was associated with increased genetic differentiation over short geographical distances. With few exceptions, each catchment contained a unique suite of species, suggesting that catchments may form hydrological barriers to gene flow, resulting in local speciation events.

Molecular diversity of Dunedin peripatus (Onychophora: Peripatopsidae)

Onychophora tend to be morphologically conservative. Several studies using molecular techniques have revealed the existence of cryptic species and population structuring. The application of allozyme electrophoresis to New Zealand peripatus that were thought to belong to a single widespread species (Peripatoides novaezealandiae) has revealed several undetected species, including a taxon specific to Dunedin (southern South Island, New Zealand). However, almost nothing is known about the geographic range and variability of this species, nor indeed whether it comprises one or more cryptic taxa. I used analysis of cytochrome oxidase I mtDNA sequences to explore these aspects of peripatus found in the vicinity of Dunedin. Eighteen different haplotypes were detected in 47 individuals from 21 locations. The sequence of a 540 bp COI fragment contained 64 parsimony informative sites and nucleotide diversity of up to 11% among ingroup taxa. Phylogenetic analyses, and genetic distance by geographic distance correlation, indicated probable species‐level divisions within the sample. Two principal groups with a boundary on the east coast of New Zealand near the mouth of the Taieri River can be defined, and these are denoted “Dunedin” and “Catlins” peripatus. There is a third, possibly distinct lineage at Piano Flat. A rearrangement of the mito‐chondrial genome, relating to the position of the tLEU rna gene, was detected in these and other New Zealand peripatus and may be present in all Onychophora.

Speciation and phylogeography of Hawaiian terrestrial arthropods.

The Hawaiian archipelago is arguably the world's finest natural laboratory for the study of evolution and patterns of speciation. Arthropods comprise over 75% of the endemic biota of the Hawaiian Islands and a large proportion belongs to species radiations. We classify patterns of speciation within Hawaiian arthropod lineages into three categories: (i) single representatives of a lineage throughout the islands; (ii) species radiations with either (a) single endemic species on different volcanoes or islands, or (b) multiple species on each volcano or island; and (iii) single widespread species within a radiation of species that exhibits local endemism. A common pattern of phylogeography is that of repeated colonization of new island groups, such that lineages progress down the island chain, with the most ancestral groups (populations or species) on the oldest islands. While great dispersal ability and its subsequent loss are features of many of these taxa, there are a number of mechanisms that underlie diversification. These mechanisms may be genetic, including repeated founder events, hybridization, and sexual selection, or ecological, including shifts in habitat and/or host affiliation. The majority of studies reviewed suggest that natural selection is a primary force of change during the initial diversification of taxa.

Relationships among palearctic Hyla: Insights from immunology

The European or green tree frog, Hyla arborea (family Hylidae; subfamily Hylinae), was once believed to be a single widespread species ranging throughout Europe and Asia. Based on data from more detailed studies of morphology and mating call, and information from molecular techniques, H. arborea is now recognized as a superspecies group. To examine relationships among these frogs, we used the quantitative immunological technique of micro-complement fixation to estimate the degree of amino acid sequence divergence in the proetin serum albumin. We estimate the divergence time between the European H. arborea and the Middle Eastern H. savignity to be about 6 MYA, while some Asian species appear to have diverged much earlier, approximately 24 MYA. Several distinct patterns of albumin cross-reactivity to the two antisera used in this study were observed. The groups distinguished by these patterns are consistent with patterns of speciation that can be supported by biogeographical history.

Taxonomic Status of Hylomys parvus and Hylomys suillus (Insectivora: Erinaceidae): Biochemical and Morphological Analyses

The genus Hylomys was thought to be represented by a single widespread species. Biochemical and morphometric analyses of several Southeast Asian populations reveal that Sumatra is inhabited by two distinct species, the dwarf gymnure ( H. parvus ) and the lesser gymnure ( H. suillus ). The absence of interbreeding between these two groups along with their relatively ancient common origins are documented by several diagnostic loci and a large Nei's genetic distance (D = 0.353 ± 0.035). The dwarf gymnure has been reported only from the slopes of the Mt. Kerinci volcano in Sumatra, where the species lives at higher elevations than its potential competitor, the lesser gymnure. Other populations of Hylomys from Java, Borneo, and Malaysia are more closely related to the Sumatran sample of H. suillus , but they exhibit strong interpopulational genetic differentiation (D = 0.165 ± 0.040) that may be accounted for by their isolated montane habitat. In addition, a principal-components analysis based on 16 measurements of the skull clearly separates adult specimens of both species. There is little overlap in the measurements between H. suillus (which is larger) and H. parvus . On Sumatra where both species may be sympatric, the notched space between premaxillary tips, soft texture of the fur, and more delicate skull and dentition are diagnostic of H. parvus .

Relationships between Coastal South American King and Blue-Eyed Shags

The distributions of King and Blue-eyed Shags (Phalacrocorax albiventer and P. atriceps) were reevaluated, incorporating new data. The differential distributions of the phenotypes do not correlate significantly with austral summer water temperatures. In areas where the forms occur together, hybridization is frequent and plumage-based disassortative mating occurs. At localities of overlap, King and Blue-eyed Shags are virtually identical in skeletal size and shape. Heterozygosity is very similar for both forms over all populations and at Puerto Deseado, but not for the Monte Le6n and Ushuaia populations. Genetic distances between the two forms are very low. King and Blue-eyed Shags should be considered conspecific color morphs of a single widespread species, Phalacrocorax atriceps.

The Sida cuneifolia-Complex (Malvaceae) in Africa

Summary. The Sida cuneifolia-complex-usually considered to consist of a single widespread species only-is shown to consist of six distinct species: S. cuneifolia Roxb. endemic to India and five species in Africa. Four of the African species are without validly published names and are described here: S. massaica, S. tanaensis, S. shinyangensis and S. tenuicarpa. Sida schimperiana A. Rich. (1847) was described from a Schimper-collection from Ethiopia. For the next 100 years this name was used for all African material belonging to this complex. Clement (1957)-while working on N American Sida commented upon the similarity between S. schimperiana and S. cuneifolia Roxb., an Indian species described in 1832. Clement considered the two to be the same species, a view which has since then been generally accepted by botanists working on African floras-Cufodontis (1959), Hauman (1963), Agnew (1974). My interest in this group stems from my work with Malvaceae for the Flora of Ethiopia. It soon became clear that the Ethiopian material of 'S. cuneifolia' could be divided into two quite distinct taxa with no intermediate collections whatsoever. Examination of East African material showed that both Ethiopian taxa were widespread in Kenya and northern Tanzania, but also revealed here three further taxa all considerably more restricted in their distribution. All these five taxa are separable by differences in structure and sculpturing of the mericarps as well as by differences in indumentum and flower-size, and I see no reason not to consider them as distinct species. Comparison of these species with the true S. cuneifolia from India shows this to be another quite distinct species which is not identical with any of those from Africa. (Fig. 1.) The group is well-defined within Sida. The species are small shrubs or shrubby herbs with cuneate to obovate leaves with a notched apex with a central tooth (extension of the midrib). The leaves are otherwise entire or have a few apical teeth (Fig. 1). The flowers are subsessile or shortly pedicelled, solitary in the leaf-axils and usually also congested into terminal heads. The corolla is pale yellow to orange, often with reddish veins. The fruit consists of five mericarps.

Latitudinal Variation in Breeding Productivity of the Rough-Winged Swallow

PRODUCTIVITY and turnover in bird populations has been the subject of lively discussion and debate for more than 20 years, since Lack (1947, 1948) formally introduced the problem of clutch size variation into the literature. It has frequently been pointed out that one cannot measure relative turnover rates in populations simply by the number of eggs laid in a clutch. Other factors, such as the survival of the young and the number of broods raised per season, are also crucial components of the population equation. Because requisite data for survival and productivity are difficult to obtain for most species, a more direct approach to measuring recruitment seemed desirable. If one could assess the ratio of immature to adult birds in a population at the proper time of the year, i.e. after the survival rates of young of the year had reached adult levels, it would be possible to estimate the annual recruitment rate of the population by the proportion of first-year birds among the breeding population (Snow, 1956). This report summarizes an effort to measure recruitment rates in a single widespread species, the Rough-winged Swallow (Stelgidopteryx ruficollis). Because birds of the year cannot be distinguished from adults after their first fall, accurate estimates of annual recruitment are not possible. The method has nonetheless revealed latitudinal gradients in fledgling productivity and suggests that, for suitable species, annual population turnover may be estimated directly from museum collections. A large geographical and seasonal series of museum specimens was examined to determine ratios of immature to adult individuals in a population. The relationship of these estimates to actual recruitment rates depends on certain assumptions about the ecology of the species and about the behavior of collectors in the field. First one must be sure that age, i.e. first year vs. adult, can be determined for museum specimens. One must also ascertain that collectors do not prefer one age class to another. To be conservative, the impartiality of the collector cannot be relied upon, but rather one must choose species that the collector cannot age until the birds are in the hand. Collectors pose additional problems with the seasonality of their activities. As recruitment estimates are based on ratios that may be obtained at any suitable point in time, seasonal bias in samples does not limit the accuracy of the estimate so much as it may cause frustration by the unavailability of data for the entire year. Assuming that one can find a suitably wide-ranging species