Genetic and morphological differentiation of the mangrove crab Perisesarma guttatum (Brachyura: Sesarmidae) along an East African latitudinal gradient

The genetic structure and morphometric differentiation of mangrove crab Perisesarma guttatum populations were examined among shelf connected locations along a latitudinal gradient on the East African coast. Over 2200 specimens were sampled from 23 mangrove sites for geometric morphometrics analysis. Population genetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences were used to evaluate connectivity among populations. A total of 73 haplotypes were detected, and almost no haplotypes were found in common between two highly supported phylogeographic clades: southern Mozambique (Inhaca Island and Maputo Bay) and a northern clade that included north Mozambique, Tanzania and Kenya. These two clades were identified based on the species' populations pairwise genetic differentiation and geographical location. Φ_ST values were considerably high between the two clades, indicating the presence of significant population genetic structure between Kenya and South Mozambique. However, each clade was composed of genetically similar populations along the latitudinal gradient, and no significant population structure was found within each clade because the Φ_st values were not significant. The morphometric analysis corroborated the division into two clades (i.e. Inhaca Island/Maputo Bay and northern populations) and also detected less shape variation among populations that were few kilometres apart. The significant spatial genetic structuring between the southern and the northern populations of P. guttatum along the geographic gradient under study, combined with morphological differences, suggests that these populations may be considered as cryptic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 28–46.     

Genetic and morphological differentiation patterns between sister species: the case of Onthophagus taurus and Onthophagus illyricus (Coleoptera, Scarabaeidae)

The present study investigated the morphological and genetic differentiation pattern between two sympatric dung beetle sister species, Onthophagus taurus and Onthophagus illyricus . The geometric morphometric approach coupled with the use of molecular markers allowed examination of the nature of interspecific relationships and an outline of the evolutionary and geographical processes that might have led to interspecific differentiation and the present-day partial sympatric and syntopic pattern of distribution. Geometric morphometrics failed to discrimininate the two species on the ground of external morphological traits, but revealed interspecific differences when the shape of the primary sexual traits was taken into account. The use of two different molecular markers (cytochrome oxidase subunit I gene and amplified fragment-length polymorphism) demonstrates that the two species are genetically well differentiated, forming two distinguishable lineages probably diverged during the Pliocene by allopatric speciation. No evidence of past or recent introgression and no support for hybridization were found, suggesting that sympatry was established subsequently, when speciation was accomplished. Both molecular markers and genital shape indicate that phenotypically intermediate individuals, despite their ambiguous appearance, are members of O. illyricus species rather than hybrids.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 197–211.     

Global patterns of population genetic differentiation in seed plants

Evaluating the factors that drive patterns of population differentiation in plants is critical for understanding several biological processes such as local adaptation and incipient speciation. Previous studies have given conflicting results regarding the significance of pollination mode, seed dispersal mode, mating system, growth form and latitudinal region in shaping patterns of genetic structure, as estimated by F_ST values, and no study to date has tested their relative importance together across a broad scale. Here, we assembled a 337‐species data set for seed plants from publications with data on F_ST from nuclear markers and species traits, including variables pertaining to the sampling scheme of each study. We used species traits, while accounting for sampling variables, to perform phylogenetic multiple regressions. Results demonstrated that F_ST values were higher for tropical, mixed‐mating, non‐woody species pollinated by small insects, indicating greater population differentiation, and lower for temperate, outcrossing trees pollinated by wind. Among the factors we tested, latitudinal region explained the largest portion of variance, followed by pollination mode, mating system and growth form, while seed dispersal mode did not significantly relate to F_ST. Our analyses provide the most robust and comprehensive evaluation to date of the main ecological factors predicted to drive population differentiation in seed plants, with important implications for understanding the basis of their genetic divergence. Our study supports previous findings showing greater population differentiation in tropical regions and is the first that we are aware of to robustly demonstrate greater population differentiation in species pollinated by small insects.     

Genetic and morphological variation in two littorinid gastropods: evidence for recent population expansions along the East African coast

In marine species, population diversity and differentiation is affected by the population history and by the complex interaction between oceanographic dynamics and ecological traits. In the present study, we examined two species of marine gastropods (the mangrove periwinkle Littoraria scabra and the rocky shore Littoraria glabrata) along the East African coast, using both genetic and geometric morphometric methods. We report a greater variation of shell shape in L. scabra compared to the slightly smaller variation in L. glabrata. This variation was probably associated with variation of environmental factors along the coast, such as temperature and hydrodynamics. Despite morphological variation, we found low mitochondrial genetic differentiation among samples from different localities for both species, which is probably a consequence of the ongoing gene flow during the free‐swimming larval stage of these gastropods. Additionally, high levels of haplotype diversity, low nucleotide diversity, and ‘star‐like’ genealogies were found in both species. These observations and the results from mismatch distributions, indicate a possible signature of recent population expansions in both species, which probably started during interglacial periods of the Pleistocene and led to the colonization of the Indian Ocean coast. © 2013 The Linnean Society of London     

High molecular and phenotypic diversity in the Merodon avidus complex (Diptera,Syrphidae): cryptic speciation in a diverse insect taxon

This paper examines molecular and phenotypic variability in the widely spread European hoverfly species complex Merodon avidus. Herein, based on the mitochondrial DNA (mtDNA) sequences of the cytochrome c oxidase subunit I (COI) and morphometric wing parameters, M. avidus is shown to comprise a complex of cryptic species, and one variety is redefined as a valid species: M. bicolor Gil Collado, 1930 (as var. of spinipes). The species M. bicolor, M. avidus A, and M. avidus B were clearly delimited based on their wing size. A total of 29 M. avidus and M. bicolor individuals presented 20 mtDNA haplotypes, four of which were shared by M. avidus A and M. avidus B, three were confined to M. bicolor, seven to M. avidus A, and six to M. avidus B. Sequence divergences between lineages occurring in the Balkan and in Spain ranged from 4.93 to 6.0 (uncorrected p in %) whereas divergences between M. avidus A and M. avidus B were 0.26 to 1.56. Divergence among morphologically identified individuals of M. avidus A and M. avidus B species ranged from 0.13 to 1.58, and from 0.13 to 0.52, respectively. The phenotypic substructuring and observed genetic uniqueness of populations in spatially and temporally fragmented M. avidus taxa were used to identify genetic units. The early split of two allopatric lineages, Spanish M. bicolor and Balkan M. avidus, was followed by diversification in each lineage. Present‐day morphological uniformity masks much of the genetic complexity of lineages within the M. avidus complex. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 819–833.     

Lack of genetic differentiation in the fat snook Centropomus parallelus (Teleostei: Centropomidae) along the Brazilian coast

The patterns of genetic variation in a fragment of the cytochrome b mtDNA gene in 130 individuals of the fat snook (Centropomus parallelus) did not show evidence of genetic differentiation along the Brazilian coast as shown in F‐statistics and AMOVA analyses, indicating the existence of high gene flow among the studied populations. In addition, the study of the evolutionary demography of the species using mismatch distribution analysis and statistical tests such as Tajima’s D and Fu’s F indicate that it experienced a pattern of population expansion during its recent evolutionary history.     

Geographic and gender shape differences in the carapace of Liocarcinus depurator (Brachyura: Portunidae) using geometric morphometrics and the influence of a digitizing method

The current work describes the use of geometric morphometrics in the study of the portunid crab Liocarcinus depurator carapace shape variation along the Mediterranean coast of Spain. As a first step, the differences in shape induced by digitizing the carapace with either a digital camera or a flat bed scanner were investigated. Carapace shape information inferred from the camera images proved different from that obtained from the scanner images. This difference was greater than any shape variation because of crab gender or sample location. Carapace shape was analysed using multiple analysis of covariance (with centroid size as a covariate) of the partial warps and uniform components indicating differences between genders and between sample location; however, significant three-way interaction implied that such differences were gender and location specific. Landmarks identifying carapace width, carapace length and posterior carapace width showed greatest variation; hence gender and location differences were further analysed through the interrelationships between these linear measures. Regression analysis of the relationship between posterior carapace width and the ratio of carapace width to carapace length indicated clear differences between locations but not between genders. Crabs from the Alborán Sea had proportionally wider posterior carapaces than those from Alicante or North Catalonia. This finding may represent the difference between a southern influx of an Atlantic population distinguishable from a more northerly Mediterranean one, which would be in agreement with the overall oceanographic surface circulation pattern in the western Mediterranean.     

Insights on the history of the scorched mussel Brachidontes rodriguezii (Bivalvia: Mytilidae) in the Southwest Atlantic: a geometric morphometrics perspective

Some authors support the idea that an important part of the Miocene marine mollusc fauna is still represented in the Argentinean Province. The fossil mollusc Brachidontes lepida (Philippi) is considered a subspecies of the extant B. rodriguezii (d?Orbigny), a taxon currently present in the Argentinean Biogeographic Province. The aim of this study is to investigate the shell shape relationship between B. lepida and B. rodriguezii using geometric morphometrics. Samples of B. rodriguezii (n = 63) from four localities distributed in Uruguay and Argentina, of B. lepida from the Paraná Formation (n = 26) and of two other extant Brachidontinae present in the region were included in this study. Canonical variate analyses showed that extant species differed in shell shape, with the discriminant function properly allocating 93% of the individuals to their respective species. Using the extant discriminant function, approximate 92% of B. lepida individuals were allocated to B. rodriguezii. This result suggests that B. lepida is more similar in shell shape to B. rodriguezii than to the other extant species present in the region. Considering the material from the Pliocene of Cerro Laciar and from the Pleistocene deposits of Buenos Aires and Bustamante, the presence of B. rodriguezii from the Late Miocene in the warm temperate region is discussed.     

Evidence of genetic distinction and long-term population decline in wolves (Canis lupus) in the Italian Apennines

Historical information suggests the occurrence of an extensive human-caused contraction in the distribution range of wolves (Canis lupus) during the last few centuries in Europe. Wolves disappeared from the Alps in the 1920s, and thereafter continued to decline in peninsular Italy until the 1970s, when approximately 100 individuals survived, isolated in the central Apennines. In this study we performed a coalescent analysis of multilocus DNA markers to infer patterns and timing of historical population changes in wolves surviving in the Apennines. This population showed a unique mitochondrial DNA control-region haplotype, the absence of private alleles and lower heterozygosity at microsatellite loci, as compared to other wolf populations. Multivariate, clustering and Bayesian assignment procedures consistently assigned all the wolf genotypes sampled in Italy to a single group, supporting their genetic distinction. Bottleneck tests showed evidences of population decline in the Italian wolves, but not in other populations. Results of a Bayesian coalescent model indicate that wolves in Italy underwent a 100- to 1000-fold population contraction over the past 2000-10,000 years. The population decline was stronger and longer in peninsular Italy than elsewhere in Europe, suggesting that wolves have apparently been genetically isolated for thousands of generations south of the Alps. Ice caps covering the Alps at the Last Glacial Maximum (c. 18,000 years before present), and the wide expansion of the Po River, which cut the alluvial plains throughout the Holocene, might have provided effective geographical barriers to wolf dispersal. More recently, the admixture of Alpine and Apennine wolf populations could have been prevented by deforestation, which was already widespread in the fifteenth century in northern Italy. This study suggests that, despite the high potential rates of dispersal and gene flow, local wolf populations may not have mixed for long periods of time.     

Evolution along the Great Rift Valley: phenotypic and genetic differentiation of East African white‐eyes (Aves,Zosteropidae)

The moist and cool cloud forests of East Africa represent a network of isolated habitats that are separated by dry and warm lowland savannah, offering an opportunity to investigate how strikingly different selective regimes affect species diversification. Here, we used the passerine genus Zosterops (white‐eyes) from this region as our model system. Species of the genus occur in contrasting distribution settings, with geographical mountain isolation driving diversification, and savannah interconnectivity preventing differentiation. We analyze (1) patterns of phenotypic and genetic differentiation in high‐ and lowland species (different distribution settings), (2) investigate the potential effects of natural selection and temporal and spatial isolation (evolutionary drivers), and (3) critically review the taxonomy of this species complex. We found strong phenotypic and genetic differentiation among and within the three focal species, both in the highland species complex and in the lowland taxa. Altitude was a stronger predictor of phenotypic patterns than the current taxonomic classification. We found longitudinal and latitudinal phenotypic gradients for all three species. Furthermore, wing length and body weight were significantly correlated with altitude and habitat type in the highland species Z. poliogaster. Genetic and phenotypic divergence showed contrasting inter‐ and intraspecific structures. We suggest that the evolution of phenotypic characters is mainly driven by natural selection due to differences in the two macro‐habitats, cloud forest and savannah. In contrast, patterns of neutral genetic variation appear to be rather driven by geographical isolation of the respective mountain massifs. Populations of the Z. poliogaster complex, as well as Z. senegalensis and Z. abyssinicus, are not monophyletic based on microsatellite data and have higher levels of intraspecific differentiation compared to the currently accepted species.     

Investigating population differentiation in a major African agricultural pest: evidence from geometric morphometrics and connectivity suggests high invasion potential

The distribution, spatial pattern and population dynamics of a species can be influenced by differences in the environment across its range. Spatial variation in climatic conditions can cause local populations to undergo disruptive selection and ultimately result in local adaptation. However, local adaptation can be constrained by gene flow and may favour resident individuals over migrants—both are factors critical to the assessment of invasion potential. The Natal fruit fly (Ceratitis rosa) is a major agricultural pest in Africa with a history of island invasions, although its range is largely restricted to south east Africa. Across Africa, C. rosa is genetically structured into two clusters (R1 and R2), with these clusters occurring sympatrically in the north of South Africa. The spatial distribution of these genotypic clusters remains unexamined despite their importance for understanding the pest's invasion potential. Here, C. rosa, sampled from 22 South African locations, were genotyped at 11 polymorphic microsatellite loci and assessed morphologically using geometric morphometric wing shape analyses to investigate patterns of population structure and determine connectedness of pest‐occupied sites. Our results show little to no intraspecific (population) differentiation, high population connectivity, high effective population sizes and only one morphological type (R2) within South Africa. The absence of the R1 morphotype at sites where it was previously found may be a consequence of differences in thermal niches of the two morphotypes. Overall, our results suggest high invasion potential of this species, that area‐wide pest management should be undertaken on a country‐wide scale, and that border control is critical to preventing further invasions.     

Intraspecific molecular phylogeny and phylogeography of the Meriones meridianus (Rodentia: Cricetidae) complex in northern China reflect the processes of desertification and the Tianshan Mountains uplift

The phylogeographical patterns and demographic history of mitochondrial DNA (cytochrome b, N = 327; D‐loop, N = 252) and nuclear DNA (IRBP gene, N = 235) haplotypes were studied for the Meriones meridianus complex in northern China, a desert‐dwelling gerbil species complex. The phylogenetic analyses, which were performed on the separate and combined (mitochondrial + nuclear) datasets, revealed two divergent clades (Clade A and Clade B) corresponding to distinct geographical regions. Clade A contained the haplotypes found mostly in individuals from the Tianshan Mountains area. Clade B contained haplotypes from populations located in other deserts in northern China. The divergence times indicated that the history of the M. meridianus complex was influenced by the uplift of the Tianshan Mountains and climate‐induced habitat fluctuations. In the Pleistocene, the expansion of forests and grasslands during interglacial period led to the isolation of the M. meridianus complex, which preferred to inhabit deserts. Hence, long geological isolation and the M. meridianus complex adaptation to local ecological conditions led to its genetic divergence. Clade A had long‐lasting demographic stability, most likely because the populations of this clade remained in a stable desert environment for a long time. However, the extension of other deserts and disappearance of palaeolakes during the last glacial period resulted in demographic expansion of Clade B. Furthermore, our genetic data indicated that two subspecies may exist within the M. meridianus complex. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 362–383.     

Heterogeneity within the native range: population genetic analyses of sympatric invasive and noninvasive clades of the freshwater invading copepod Eurytemora affinis

Invasive species are often composed of highly differentiated populations or sibling species distributed across their native ranges. This study analysed patterns of distribution and the evolutionary and demographic histories of populations within the native range of the copepod species complex Eurytemora affinis. Genetic structure was analysed for samples from 17 locations from both the invaded and native ranges in the St Lawrence River drainage basin, using 652 base pairs of the mitochondrial cytochrome oxidase subunit I gene. This study revealed a high degree of heterogeneity in genetic structure and habitat type in the native range, as well as a bias in the sources of invasive populations. Two genetically distinct clades showed a pattern of niche partitioning within the St Lawrence basin. The noninvasive North Atlantic clade primarily occupied the central portion of the St Lawrence Middle Estuary, whereas the invasive Atlantic clade was more prevalent along the margins, in the upstream reaches of the estuary and downstream salt marshes. Habitat partitioning and genetic subdivision was also present within the Atlantic clade. The freshwater populations were genetically more proximate to the Atlantic clade populations in the estuary than to those in the salt marsh, suggesting the estuary as the source of the invasive populations. The freshwater invading populations showed evidence of a modest population bottleneck. Populations from both clades showed genetic signatures of demographic population expansions that preceded the timing of the last glacial maximum, supporting the St Lawrence as a secondary contact zone between the two clades. Additional analyses on physiological and evolutionary properties of populations in the native range, along with analysis of the selection regime within native habitats, might yield insights into the evolutionary potential to invade.     

Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States

Analysing the population genetic structures of sympatric species provides opportunities to compare patterns of population genetic structure and phylogeography in order to gain insight into the factors that influence the development of the observed patterns. In this study, we compared the population genetic structures and phylogeographies of brown shrimp (Farfantepenaeus aztecus) and white shrimp (Litopenaeus setiferus), two sympatric penaeid shrimp species that inhabit the waters of the eastern USA, using sequence analysis of the mitochondrial DNA control region. Brown shrimp showed no significant phylogenetic structure or population subdivision, and closely related haplotypes were geographically dispersed. Mismatch analysis indicated that brown shrimp experienced a late-Pleistocene era sudden population expansion. In contrast, white shrimp had a complex haplotype phylogeny consisting of two distinct lineages and two less well-defined sublineages, and the haplotypes and lineages were geographically structured. Mismatch analysis for white shrimp also showed evidence of sudden population expansion, albeit for each lineage separately and more recently than in the brown shrimp. These disparate patterns may have developed as a result of species-specific differences in physiological tolerances and habitat preferences that caused greater fluctuations in white shrimp population sizes and reductions in long-term effective population size relative to that of the brown shrimp, and thereby increased the susceptibility of the white shrimp populations to stochastic genetic change.     

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa

The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio‐ and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP‐ and mtDNA‐tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.     

Assessing the genetic diversity and population structure of Culter alburnus in China based on mitochondrial 16S rRNA and COI gene sequences

The genetic diversity and population genetic structure of Culter alburnus were investigated using mitochondrial cytochrome c oxidase subunit I (COI) and ribosomal 16S subunit (16S rRNA) gene sequences. A total of 89 individuals from four localities were included in the analysis. Overall, 12 polymorphic sites were observed and 10 haplotypes were defined. The C. alburnus populations were characterized by high haplotype diversity (0.587 ± 0.047) and low nucleotide diversity (0.00197 ± 0.00073). Pairwise fixation index (F_ST) analysis indicated significant genetic differentiation among different populations. The hierarchical analysis of molecular variance (AMOVA) analysis also showed significant genetic divergence (φ_ST = 0.3792, P < 0.01) among these populations. The present results suggest that subdivisions exist among four C. alburnus populations, and should be considered as different management unit for effective conservation and management purposes. This study provides new information for genetic assessment and will be crucial for establishing fisheries management and strategies for this species.     

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation

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