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PubMed2001

Phylogeography of the tidewater goby, Eucyclogobius newberryi (Teleostei, Gobiidae), in coastal California.

The tidewater goby, Eucyclogobius newberryi, inhabits discrete, seasonally closed estuaries and lagoons along approximately 1500 km of California coastline. This species is euryhaline but has no explicit marine stage, yet population extirpation and recolonization data suggest tidewater gobies disperse intermittently via the sea. Analyses of mitochondrial control region and cytochrome b sequences demonstrate a deep evolutionary bifurcation in the vicinity of Los Angeles that separates southern California populations from all more northerly populations. Shallower phylogeographic breaks, in the vicinities of Seacliff, Point Buchon, Big Sur, and Point Arena segregate the northerly populations into five groups in three geographic clusters: the Point Conception and Ventura groups between Los Angeles and Point Buchon, a lone Estero Bay group from central California, and San Francisco and Cape Mendocino groups from northern California. The phylogenetic relationships between and patterns of molecular diversity within the six groups are consistent with repeated, and sometimes rapid, northward and southward range expansions out of central California caused by Quaternary climate change. Plio-Pleistocene tectonism, Quaternary coastal geography and hydrography, and historical human activities probably also influenced the modern geographic and genetic structure of E. newberryi. The phylogeography of E. newberryi is concordant with phylogeographic patterns in several other coastal California taxa, suggesting common extrinsic factors have had similar effects on different species. However, there is no evidence of a phylogeographic break coincident with a biogeographic boundary at Point Conception.

Animals↗
PubMed2003

Linear habitats and the nested clade analysis: an empirical evaluation of geographic versus river distances using an Ozark crayfish (Decapoda: Cambaridae).

The nested clade analysis can be extremely useful in testing for an association between genetic variation and geography and in explaining these observed patterns in terms of historical or contemporary population processes. The strength of this method lies in its ability to test a variety of processes simultaneously under a rigorous statistical framework. Indeed, many recent studies have used the nested analysis in a wide range of terrestrial and aquatic taxa. However, it has been suggested that riverine, riparian, or coastal species may be better examined using river (or coastal) distances rather than the standard geographic (great circle) distances among populations. It is thought that the standard geographic distances may not adequately describe the actual distances involved between populations of species inhabiting these one-dimensional (riverine) habitats. Therefore, we analyzed population data from an Ozark crayfish, Orconectes lutetus, to examine the effects on the results of a nested clade analysis using river distances. In most cases, the haplotypes detected in this crayfish were unique to a particular drainage or a group of neighboring drainages, indicating very little movement of individuals among drainages. Five major population groups were detected, corresponding to many of the major river drainages sampled in this study. The two types of distance analyses obtain similar results for higher-level (older) clades, but differ in many of the inferences made for lower-level (younger) clades. However, we suggest that the comparison of both types of analyses for riverine species may enhance the process of elucidating historical and contemporary population processes, especially in cases where the transfer of individuals among different drainages are involved.

Animals↗
PubMed2004

Speciation on the coasts of the new world: phylogeography and the evolution of bindin in the sea urchin genus Lytechinus.

Beginning with E. Mayr's study in 1954, tropical sea urchins have played an important role in studies of speciation in the sea, but what are the processes of cladogenesis and divergence that give rise to new species in this group? We attempt to answer this question in the genus Lytechinus. Unlike the majority of other tropical sea urchin genera, which have circumtropical distributions, Lytechinus is mostly confined to the tropics and subtropics of the New World. We sequenced a region of mitochondrial cytochrome oxidase I and the entire molecule of nuclear bindin (a sperm gamete recognition protein) of nearly all species in the genus, and we assayed isozymes of three partially sympatric closely related species and subspecies. We found that in both mitochondrial DNA (mtDNA) and in bindin the genus Lytechinus is paraphyletic, encompassing Sphaerechinus granularis as the sister species of L. euerces. The rest of the species are arranged in an Atlantic clade composed of L. williamsi and L. variegatus, and a Pacific clade containing L. anamesus, L. pictus, L. semituberculatus, and L. panamensis. Divergence between these clades suggests that they were separated no later than the closure of the Isthmus of Panama, and possibly before this time. Our data confirm that L. anamesus and L. pictus from California are a single species, and provide no evidence of differentiation between L. variegatus variegatus from the Caribbean and L. variegatus atlanticus from Bermuda. Lytechinus variegatus variegatus mtDNA is distinct from that of L. variegatus carolinus from the North American seaboard and the Gulf of Mexico, whereas their bindins are very similar. However, there is clear evidence of introgression of mtDNA between the two subspecies and they share alleles in all sampled isozyme loci. Lytechinus williamsi from the Caribbean shares mtDNA haplotypes with L. variegatus variegatus, and they also share isozymes in all assayed loci. Their bindin, however, is distinct and coalesces within each morphospecies. A private clade of mtDNA in L. williamsi may be indicative of former differentiation in the process of being swamped by introgression, or of recent speciation. Recent sudden expansions in effective population size may explain the predominance of a few mitochondrial haplotypes common to the two species. Despite the high divergence of bindin (relative to differentiation of mtDNA) between L. variegatus and L. williamsi, comparison of amino acid replacement to silent substitutions by various methods uncovered no evidence for positive selection on the bindin of any clade of Lytechinus. With the possible exception of L. williamsi and L. variegatus, our results are consistent with a history of allopatric speciation in Lytechinus. The molecular results from Lytechinus, along with those of other similar studies of sea urchins, suggest that the general speciation patterns deduced in the middle of last century by Mayr from morphology and geography have held up, but also have uncovered peculiarities in the evolution of each genus.

Americas↗
PubMed2004

Population structure of the beetle pests Phyllodecta vulgatissima and P. vitellinae on UK willow plantations.

Phyllodecta (= Phratora) vulgatissima and P. vitellinae (Coleoptera: Chrysomelidae) are important pests of willows and poplars. Their differences in host species preference may provide a non-chemical control strategy for pest control. However, little is known about population structure with respect to hosts, regions or seasons. Using five microsatellites, 850 P. vulgatissima and 1100 P. vitellinae individuals, comprising 17 and 22 UK samples, respectively, were genotyped. High diversity was observed at all loci. Migrant numbers exchanged per generation (Nm) were high (2.1-12.6 for P. vulgatissima and 0.9-12.2 for P. vitellinae), suggesting high genetic exchange between samples. Estimates of population differentiation (FST) and analyses of the data using Bayesian methods (Partition and Structure) showed little evidence of subdivision in relation to geography, sampling time or host.

Animals↗
PubMed2004

Speciation, phylogeography and evolution of life history and morphology in plethodontid salamanders of the Eurycea multiplicata complex.

Understanding the complex interactions among environment, genotype and ontogeny in determining organismal phenotypes is cental to many biological disciplines. The Eurycea multiplicata complex, endemic to the Interior Highlands (Ozark Plateau and Ouachita Mountains) of eastern North America, comprises a diverse radiation of paedomorphic surface-dwelling (E. tynerensis), metamorphic surface-dwelling (E. multiplicata multiplicata and E. m. griseogaster) and metamorphic subterranean (Typhlotriton spelaeus) hemidactyliine plethodontid salamanders. Portions of two mitochondrial genes, cytochrome-b and NADH dehydrogenase-4, totalling 1818 base pairs (bp) were sequenced for 70 ingroup individuals plus numerous outgroup taxa, to examine the biogeography and relationships among these morphologically disparate species. Results show the E. multiplicata complex to be monophyletic, with its two most divergent clades corresponding to geography, not morphology or life history. Transforming surface-dwelling populations from the Ouachitas (E. m. multiplicata) are sister to the Ozark taxa, including paedomorphic surface-dwelling (E. tynerensis), subterranean (T. spelaeus) and transforming surface-dwelling salamanders assigned to the 'subspecies'E. m. griseogaster. Among Ozark taxa T. spelaeus (deeply nested within Eurycea) is sister to a clade that includes E. m. griseogaster and E. tynerensis. Current taxonomy suggests that paedomorphic populations (E. tynerensis) from the western Ozarks are distinct from nearby transforming populations (E. m. griseogaster). However, paedomorphic and transforming salamanders do not form reciprocally monophyletic groups and many populations share almost identical haplotypes. Ancestral state reconstruction of life history traits shows that paedomorphosis arose independently from three to nine times. Most populations are either completely paedomorphic or completely transforming. This suggests that local habitat parameters strongly influence life history mode in this complex, either facultatively or by selection for particular genotypes.

Animals↗
PubMed2004

Geographic genetic architecture of pocket gopher (Thomomys bottae) populations in Baja California, Mexico.

Phylogenetic analyses of complete mitochondrial cytochrome b sequences support the monophyly of pocket gopher (Thomomys bottae) populations from the 1000 km length of the Baja California peninsula of Mexico, relative to other geographical segments of the species range in western North America. The Baja California peninsula is an area that encompasses considerable ecomorphological and infraspecific diversity within this pocket gopher species. However, detailed population analyses encompassing 35 localities distributed over the southern half of the peninsula reveal only trivial phylogeographical structure. Rather, most of the 72 unique 500-base pair haplotypes examined from 142 individuals is restricted to single populations, although a few haplotypes are shared broadly across geography. Individual populations are typically comprised of haplotype sets from different branches in a network of relationships. Analysis of molecular variance (amova) indicates that approximately half of the total pool of variation is contained among individuals within local populations, and that only about 25% can be explained by the regional subdivisions of current subspecies distributions or physiographic realms. A hypothesized historical vicariant event that has been causally linked to the phylogeographical structure of other, codistributed species has had little influence on these pocket gopher populations, explaining only 13% of the total variation. The temporal depth, estimated by coalescence parameters, of the haplotype lineage in Baja California is relatively recent, approximately 300,000 generations; both the mismatch distribution of pairwise comparisons and a significantly positive exponential growth estimate support a recent history of expanding populations; but current, or recent past, migration estimates have remained small, are largely unidirectional from north to south, and weak isolation by distance is present. All data suggest that pocket gophers have relatively recently invaded the southern half of peninsular Baja California, with the genetic signature of expansion still evident but with sufficient time having lapsed to result in a weak isolation by distance pattern. The geographical assemblage of sampled populations thus appears as a meta-population, with limited gene flow contrasting with random haplotype loss due to drift in small, localized populations.

Analysis of Variance↗
PubMed2004

Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas.

The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations.

Animals↗
PubMed2005

A role for nonphysical barriers to gene flow in the diversification of a highly vagile seabird, the masked booby (Sula dactylatra).

To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low-latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies (Sula dactylatra). In accord with previous studies, we found that Indo-Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo-Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher-level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher-level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo-Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo-Pacific populations. We estimate that Indo-Pacific masked boobies experienced rapid population growth approximately 180,000 years ago and that the majority of Indo-Pacific and Atlantic populations diverged within the last approximately 115,000 years. These combined data suggest that the predominant pattern between Indo-Pacific and Atlantic populations is long-term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.

Animals↗
PubMed2006

Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939).

The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high (h = 0.73) with pronounced population structure (Phi(ST) = 0.877) and highly significant geographic associations (P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

Animals↗
PubMed2006

Multiple introductions promote range expansion of the mollusc Cyclope neritea (Nassariidae) in France: evidence from mitochondrial sequence data.

Since the 1970s, the nassariid gastropod Cyclope neritea has been extending its range north along the French Atlantic coasts from the Iberian Peninsula. This may be due to natural spread because of the recent warming of the northeastern Atlantic. However, human-mediated introductions related to shellfish culture may also be a probable explanation for this sudden range expansion. To examine these two hypotheses, we carried out a comprehensive study based on mitochondrial gene sequences (cytochrome oxidase I) of the five recently colonized French bays as well as 14 populations located in the recognized native range of the species. From a total of 594 individuals, we observed 29 haplotypes to split into three divergent clades. In the native range, we observed a low molecular diversity, strong genetic structure and agreement between geography and gene genealogies. Along the French coasts, we observed the opposite: high genetic diversity and low genetic structure. Our results show that recurrent human-mediated introductions from several geographical areas in the native range may be a source for the French Atlantic populations. However, despite the low dispersal ability of C. neritea, the isolation-by-distance pattern in France suggested that this gastropod may have been present (although unnoticed) on the French Atlantic coasts before the 1970s. As C. neritea shows characteristics of a cryptogenic species, the classification of Atlantic populations as either native or introduced is not straightforward. Cryptogenic species should be studied further to determine the status of new populations close to their recognized native range.

Animals↗
PubMed1993

Migration regions and interstate labor flows by occupation in the United States.

"This paper investigates the migration patterns of occupational groups [in the United States]. The results confirm previous analyses of the differences in movement behavior between occupations but, in addition, show that this variation is a function of the industrial sector of employment. The chief aim of the paper, however, is to uncover the geography of labor flows for different occupational groups using a principal components analysis of interstate flow matrices....Results indicate that migration regions vary by occupation and industry and we argue that these differences reflect job information flows and regional employment structure for various classes of labor." Data are from the Public Use Microdata Sample A taken from the 1980 census.

Americas↗
PubMed1977

Bioassay of kinship in northwestern Europe.

Kinship of Barra (Outer Hebrides) is bioassayed as 0.0096 relative to northwestern Europe, in reasonable agreement with prediction of 0.008 relative to Britain. The exponential decline of kinship with distance is similar to Scandinavia. Kinship of larger populations is consistent with predictions from isolates. Kinship is largely due to local drift rather than Norse admixture, the estimate of which is obscured by drift and appears highly unreliable. Other populations in northwest Europe, including Iceland, Lewis and Orkney, give estimates of kinship which reflect drift and geography, but also do not provide reliable estimates of admixture. Bioassay of kinship from gene frequencies gives observations to be explained in terms of migration and drift, but contributes nothing to the question of whether polymorphism in the species is maintained by neutral mutation or selection. Although the latter is on various grounds more likely, no calculations based on gene frequency distribution can provide critical evidence.

Emigration and Immigration↗
PubMed2006

Geographical variations in TP53 mutational spectrum in ovarian carcinomas.

The TP53 gene mutational spectrum in human tumours shows variations related to tissue of origin, carcinogen exposure or molecular background. We have compared TP53 mutations in ovarian carcinomas from different geographical regions; this study was based on data extracted and verified from the IARC database (R10, 2005), and on our results from 127 carcinomas. In total 873 mutations were evaluated. Tumours from Japan and Korea had a higher frequency of exon 7 mutations (38%vs 25%, p = 0.011) and lower frequency of exon 8 mutations (11%vs 29%, p = 0.0003) than those from Western countries; they were particularly different from Norwegian tumours which showed the lowest proportion of exon 7 (19%, p = 0.001) and highest proportion of exon 8 (37%, p < 0.0001) mutations. There were also differences in the profile of TP53 hotspots. The third hotspot in tumours from Poland was amino acid (AA) 176 (8.2% of substitutions vs 1.7% in other countries, p < 0.001), while in tumours from the UK it was AA 220 (8.9%vs 2.3%, p < 0.001). Codon 273 was the only apparent hotspot in the Norwegian tumours, while it was rarely mutated in Polish and Asian tumours. In contrast to other data tumours from Norway presented with 273(HIS) codon (82% of mutations at AA 273, p = 0.002), while tumours from the UK shared the 273(CYS) codon (80%, p < 0.001). Further analysis of TP53 gene mutations in ovarian cancer by geography could provide greater insights.

Adenocarcinoma, Clear Cell↗
PubMed2006

Pseudocyphellaria crocata, P. neglecta and P. perpetua from the Northern and Southern Hemispheres are a phylogenetic species and share cyanobionts.

Pseudocyphellaria crocata, P. neglecta and P. perpetua specimens were examined to investigate links between genetic variation and morphology, geographical distribution and cyanobiont specificity. Fungal internal transcribed spacer (ITS), beta-tubulin and cyanobacterial tRNA(Leu) (UAA) intron sequences were used to investigate symbiont diversity in these lichens. Specimens were morphologically distinct but could not be distinguished by ITS sequences. Phylogenetic analyses split the P. crocata specimens into two clades, the larger of which contained P. neglecta and P. perpetua. Five cyanobionts were identified; two of these were in a number of specimens, while three were each restricted to a single lichen thallus. Fungus-specific molecular markers indicated that all specimens belonged to a single phylogenetic species. However, this may contain a cryptic species. Geography was linked to genetic diversity with Canadian specimens forming a monophyletic group, and most Southern Hemisphere specimens grouping together, although Chile represented a hot spot of genetic diversity. There was no connection between fungal genetic diversity and cyanobiont choice, consistent with the presence of a common pool of cyanobionts.

Ascomycota↗
PubMed1987

Modelling interprovincial migration using entropy-maximizing methods.

"The concern in this paper is with the prediction of population movements through the mathematical modelling of migration. In particular, the emphasis is on the testing of one of the most basic of a family of models of spatial interaction that have been developed in an information theoretic context in geography. Of special interest with this basic, totally constrained interaction model is the role of the distance variable in population migration and the extent to which it can be employed to predict Canadian interprovincial population migration flows."

Americas↗
PubMed2006

The unusual genetics of human longevity.

In no species other than humans do cultural, social, and biological factors interact with each other in modulating complex phenotypes. Thus, the identification of genetic factors that affect human longevity is a true challenge. The model of centenarians provides us a unique opportunity to tackle this challenge. In this Perspective, we discuss some recent findings (the impact of geography and demography on the longevity phenotype, the relationship between longevity and homozygosity, the role of the nuclear-mitochondrial genome cross-talk) by which new ideas are suggested, such as the concept of a complex allele timing as a pivotal process in modulating the probability of achieving longevity.

Demography↗
PubMed1973

Gene flow and population differentiation.

There are many possible spatial patterns of selection and gene flow that can produce a given cline structure; the actual geography of natural selection and gene flow must be worked out before an attempt is made to explain a given natural cline in terms of a model. The results of experimental and theoretical models show that it is possible for local differentiation to evolve parapatrically in spite of considerable gene flow if the selection gradients are relatively uniform. Irregularities in environmental gradients increase the sensitivity of clines to the effects of gene flow in proportion to the increase in the differences in gene frequencies between the emigrants and the demes receiving the immigrants. It is not necessary for a sharp spatial environmental change to be present for distinct differentiation to occur. In some cases even a gentle environmental gradient can give rise to marked spatial differentiation along a genetically continuous series of demes; such environmental differences may be below the practical limits of resolution in field studies. Any asymmetry in gene flow does not lead to dedifferentiation if the environmental gradient is smooth; it merely shifts the position of the transition zone between the differentiated areas from that which would be expected if there were no asymmetry. Abrupt geographic differences in gene, genotype, or morph frequencies should not, therefore, be interpreted as evidence for environmental changes in the immediate vicinity of the steepest part of the cline; neither should they be interpreted as evidence for geographic barriers, sharp environmental differences, or sexual isolation among the differentiated groups of populations when there are no other sources of evidence for these phenomena. Gene flow may be unimportant in the differentiation of populations along environmental gradients.

Animals↗
PubMed1993

Demic expansions and human evolution.

Geographic expansions are caused by successful innovations, biological or cultural, that favor local growth and movement. They have had a powerful effect in determining the present patterns of human genetic geography. Modern human populations expanded rapidly across the Earth in the last 100,000 years. At the end of the Paleolithic (10,000 years ago) only a few islands and other areas were unoccupied. The number of inhabitants was then about one thousand times smaller than it is now. Population densities were low throughout the Paleolithic, and random genetic drift was therefore especially effective. Major genetic differences between living human groups must have evolved at that time. Population growths that began afterward, especially with the spread of agriculture, progressively reduced the drift in population and the resulting genetic differentiation. Genetic traces of the expansions that these growths determined are still recognizable.

Animals↗