Cranial morphological variation among contemporary Mexicans: Regional trends,ancestral affinities,and genetic comparisons

Genetic research has documented geographical variation within Mexico that corresponds to trends in ancestry admixture from postcolonial times on. The purpose of this study is to determine whether craniometric variation among contemporary Mexicans is comparable to that reported in genetic studies. Standard osteometric measurements were taken on 82 male crania derived from forensic cases, with geographic origins of the specimens spanning over two‐thirds of Mexico's states. To study similarities in regional clustering patterns with genetic data, k‐means clustering analyses were performed, followed by chi‐square tests of association between cluster assignments and geographic region of origin. Normal mixtures analyses were performed, centered on three “ancestral” sample proxies to estimate classification probability to each ancestry. The results demonstrate that the cranial morphological sample data cluster similarly to the regional groupings inferred from the genetic data. Additionally, the results indicate a gradient trend in population structure for contemporary Mexicans, with the proportion of Amerindian ancestry increasing from North to South while, conversely, European ancestry proportion estimates increase from South to North. Furthermore, the probabilities for classification of African ancestry remained low across the regions, again reflecting the results for the genetic data. Cranial morphological variation is well aligned with the genetic data for describing broad trends among Mexican populations, as well as yielding comparable estimates of general ancestry affiliations that reflect Mexico's history of Spanish contact and colonialism. Am J Phys Anthropol 151:506–517, 2013. © 2013 Wiley Periodicals, Inc.     

Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean

Geographic barriers that limit the movement of individuals between populations may create or maintain phylogenetically discrete lineages. Such barriers are often inferred from geographic surveys of a single mitochondrial marker to identify phylogenetic splits. Mitochondrial DNA, however, has an effective population size one-fourth that of nuclear DNA, which can facilitate the rapid evolution of monophyletic mtDNA lineages in the absence of geographic barriers. The identification of geographic barriers will thus be more robust if barriers are proposed a priori, and tested with multiple independent genetic markers in multiple species. Here, we tested two proposed marine biogeographic breaks located at the Mona Passage in the Caribbean Sea and at the southern end of Exuma Sound in the Bahamas. We sequenced mitochondrial cytochrome b (400 bp) and nuclear rag1 (573 bp) for nine species and colour forms (183 individuals total) within the teleost genus Elacatinus (Gobiidae) that span the proposed breaks. Our results showed that Mona Passage separated mtcyb and rag1 lineages, with no genetic exchange between populations separated by just 23 km. However, the Central Bahamas barrier was only weakly supported by our data. Importantly, neither barrier coincided with deep genetic splits. This suggests that these two barriers did not initially isolate regional populations, but instead disrupt ongoing gene flow between regions. Our inferred relationships further suggested a division of the Caribbean region into northwestern and southeastern regions, a pattern reflected by some freshwater and terrestrial vertebrates. Our results, coupled with genetic and demographic data from other reef fishes and corals, provide robust support for the Mona Passage as a long-term biogeographic barrier for Caribbean animals.     

Determinants of reef fish assemblages in tropical Oceanic islands

Diversity patterns are determined by biogeographic, energetic, and anthropogenic factors, yet few studies have combined them into a large‐scale framework in order to decouple and compare their relative effects on fish faunas. Using an empirical dataset derived from 1527 underwater visual censuses (UVC) at 18 oceanic islands (five different marine provinces), we determined the relative influence of such factors on reef fish species richness, functional dispersion, density and biomass estimated from each UVC unit. Species richness presented low variation but was high at large island sites. High functional dispersion, density, and biomass were found at islands with large local species pool and distance from nearest reef. Primary productivity positively affected fish richness, density and biomass confirming that more productive areas support larger populations, and higher biomass and richness on oceanic islands. Islands densely populated by humans had lower fish species richness and biomass reflecting anthropogenic effects. Species richness, functional dispersion, and biomass were positively related to distance from the mainland. Overall, species richness and fish density were mainly influenced by biogeographical and energetic factors, whereas functional dispersion and biomass were strongly influenced by anthropogenic factors. Our results extend previous hypotheses for different assemblage metrics estimated from empirical data and confirm the negative impact of humans on fish assemblages, highlighting the need for conservation of oceanic islands.     

New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread

Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all such studies are based on phylodynamic models that assume—despite direct and compelling evidence to the contrary—that rates of viral geographic dispersal are constant through time. Here, we: (1) extend phylodynamic models to allow both the average and relative rates of viral dispersal to vary independently between pre-specified time intervals; (2) implement methods to infer the number and timing of viral dispersal events between areas; and (3) develop statistics to assess the absolute fit of discrete-geographic phylodynamic models to empirical datasets. We first validate our new methods using simulations, and then apply them to a SARS-CoV-2 dataset from the early phase of the COVID-19 pandemic. We show that: (1) under simulation, failure to accommodate interval-specific variation in the study data will severely bias parameter estimates; (2) in practice, our interval-specific discrete-geographic phylodynamic models can significantly improve the relative and absolute fit to empirical data; and (3) the increased realism of our interval-specific models provides qualitatively different inferences regarding key aspects of the COVID-19 pandemic—revealing significant temporal variation in global viral dispersal rates, viral dispersal routes, and the number of viral dispersal events between areas—and alters interpretations regarding the efficacy of intervention measures to mitigate the pandemic.     

New species and new records of Tinodes Curtis (Trichoptera: Psychomyiidae) from Dabie Mountains,East-central China

We describe a new Tinodes, Tinodes stamen sp. nov., collected in the Dabie Mountains, East-central China and report four new records, T. ventralis Li & Morse, 1997; T. cryptophallicata Li & Morse, 1997; T. harael Malicky, 2017; and T. sartael Malicky, 2017, from Dabie Mountains. Moreover, we illustrate infraspecific variability in T. ventralis, and the recently described T. harael, and T. sartael from the Dabie Mountains region.     

Human disturbance and natural habitat: a biome level analysis of a global data set

This paper presents an analysis of conversion of natural habitat to human use on a global scale. Human disturbance of natural systems is classified in a three-category system and ranked using a Habitat Index based on remaining undisturbed and partially disturbed land. Data is analysed by biome and biogeographic province, allowing identification of the biomes and provinces which have been the most impacted by human activity. Temperate biomes are found to be generally more disturbed than tropical biomes. Four of the top five most disturbed biomes are temperate. Certain biomes and geographic areas stand out as conservation priorities, notably the islands of Southeast Asia, Mediterranean vegetation types, Temperate Broadleaf Forests and Tropical Dry Forests. Areas for which data deficiencies exist are identified.     

Contribution of rarity and commonness to patterns of species richness in biogeographic transitions regions: Woody plants of Uruguay

There is a growing body of evidence suggesting that widespread (i.e. common) rather than geographically restricted species (i.e. rare) shape the overall distribution patterns of species richness. This is a non‐intuitive fact, given that local and regional assemblages are normally composed by numerous rare species and few common ones. We evaluated here the primacy of common species in a biogeographic transition zone, where rarity has frequently a higher incidence. We analysed the geographical variability of trees and shrubs in Uruguay, located in a transitional zone between prairie and forest biomes, to assess the relative contribution of rare and common species to the generation of richness patterns. The distribution of 301 species of the native woody assemblage of Uruguay was mapped over the national grid system (302 quadrants of approximately 22 × 30 km), using published data and herbarium records. The overall assemblage was segregated into four subassemblages in function of species distribution (quartiles). Species richness in the four quartiles was positively correlated with overall richness, but common species (quartile 3) showed the highest level of correlation. Then, we ranked species from the most widespread to the most restricted (common‐to‐rare) and from the most restricted to the most widespread (rare‐to‐common). Along each stage of the sequences we obtained a series of species richness patterns for increasing numbers of species. Correlating the species richness pattern for each subassemblage of both sequences with that of the full assemblage, we also found higher correlations in the common‐to‐rare sequence. We conclude the Uruguayan woody plants assemblage has a very large number of rare species as expected for a transitional biogeographical zone, but it was the common species that contributed most to the overall pattern of species richness. We propose the low contribution of rare species is explained by the most interspecific variability in ecological determinants within the assemblage of rare species. Therefore the spatial covariance among rare species is low, and so is the relationship with overall species richness.     

Parsimony analysis of endemicity as a panbiogeographical tool: an analysis of Caribbean plant taxa

To demonstrate that parsimony analysis of endemicity (PAE) can be a method implementing the panbiogeographic approach, we analyzed two data matrices of 40/38 biogeographic provinces × 148 plant species from the Caribbean subregion of the Neotropical region, one where taxa are represented by individual tracks and the other where taxa are represented by single sample localities. We obtained six generalized tracks resulted from the PAE of the areas × individual tracks matrix, and one generalized track from the PAE of the areas × single sample localities matrix, with the latter nested within the former tracks. The results obtained show that PAE works as a panbiogeographical tool if it is based on an areas × individual tracks matrix. When performed in this way, PAE retrieves spatial information that is lost when it is based on an areas × single sample localities matrix, raising doubts regarding the conclusions derived from this latter type of analysis. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 961–976.     

First record of forktailed bass Parasphyraenops incisus (Perciformes: Serranidae) in South‐western Atlantic

We reported the genus Parasphyraenops (Perciformes: Serranidae) in the Brazilian Biogeographic Province. Four Parasphyraenops incisus specimens were identified based in body shape and color pattern through underwater remote video records, on shallow coral reefs in the Bahia state, Brazil. In the video frames P. incisus was observed swimming close to the pomacentrid Chromis multilineata at 14 m depth, being this the shallowest record for this species. The present record expands on 6.500 km the southern limit of distribution of P. incisus in the Western Atlantic.     

Reconstruction of adaptive radiation in insular habitats using integrated biogeographic information

Aim To develop an analytical method for accurately reconstructing the biogeographic events associated with adaptive radiation in a system of insular habitats. Location An idealized, two-dimensional model system of insular habitats is based on the altitudinally stratified vegetation zones on the island-like mountains of eastern Africa. Methods The model system is treated as a two-dimensional array of insular habitats, and adaptive radiation is treated as a ‘space-filling’ process according to six premises based on uniformitarian principles. Previous approaches to this class of problems have used (1) Hennig's progression rule, (2) optimization of biogeographic character states, and (3) reasoned argumentation with an intuitive synthesis of information. The strengths and limitations of these previous approaches are evaluated. Results A closed analytical method is presented that accurately reconstructs biogeographic events. This methodological approach integrates atomized information back up to the appropriate level of biological organization and has general applicability to phylogenetic analysis. Main conclusions In a truly evolutionary approach to phylogenetic systematics and biogeography, the initial analysis of the pattern of descent should be complemented with a subsequent analysis of the pattern of modification. The method presented here offers one approach to analysing the pattern of modification, which in this case constitutes biogeographic movement.     

Fossil biogeography: a new model to infer dispersal,extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.     

Structure of communities of ground-dwelling animals at the junction of two phytogeographic zones

Changes in the structure of tenebrionid beetle, lizard and rodent communities along the aridity gradient that determines the position of a phytogeographic province boundary were studied to test: (1) whether there are two different species assemblages on either side of the boundary (2) the extent of their differentiation and (3) if they are composed of different or the same faunal elements. Several ordination methods were tested for their capacity to reflect community structure, and discriminant function analysis was selected as the primary method of ordination. Each of the ordination axes reflected a complex environmental gradient. The latter was different for each taxon. The gradient of productivity cross-cuts ecological space for each animal group in an individual manner. Revealed spatial assemblages of species were related to the level of productivity. There was one assemblage of species at high productivity and one or two assemblages occurred at low productivity in each taxon. The α–diversity curve of rodents changed weakly along the productivity gradient, whereas those of lizard and beetle communities were distinctly unimodal and had maxima near the middle of the gradient. β–diversity curves of rodents had a concave shape, but those of lizard and beetle communities increased from low productivity values to the middle of the gradient and after that weakly declined to the upper (productive) end of the gradient. Seven types of ranges or areographic groups of species were distinguished. Each species assemblage was composed of different faunal elements. Comparison of the results of ecological and areographic analyses demonstrated that two assemblages of rodents and lizards represent different guilds within the same community rather than different communities. The phytogeographic border for these taxa is an ecological rather than a geographical boundary. The difference between the two tenebrionid assemblages appears to be zoogeographical rather than ecological, and coincides with the phytogeographic boundary.     

Biotic homogeneity of putative biogeographic units in the Neotropics: A test with Sapotaceae

Aim

To evaluate Morrone's (2001, Biogeografia de America Latina y el Caribe. Zaragoza, Spain: CYTED, ORCYT‐UNESCO, Sociedad Entomológica Aragonesa (SEA)) Neotropical regionalization by testing the prediction that biotas are more homogeneous within than among biogeographic units.

Location

Neotropics.

Methods

We conducted pairwise comparisons of beta diversity of Sapotaceae species within and between biogeographic units in the hierarchical regionalization proposed by Morrone (2001, Biogeografia de America Latina y el Caribe. Zaragoza, Spain: CYTED, ORCYT‐UNESCO, Sociedad Entomológica Aragonesa (SEA)), at a spatial resolution of 1‐degree cells. We used a null model to control differences in sampling effort across 1‐degree cells and performed beta‐diversity comparisons conditional on geographic distance to control for distance decay of biotic similarity.

Results

None of the biogeographic units proposed by Morrone (2001, Biogeografia de America Latina y el Caribe. Zaragoza, Spain: CYTED, ORCYT‐UNESCO, Sociedad Entomológica Aragonesa (SEA)) was biotically homogeneous with respect to all other units at the same hierarchical level. This was the case even for units commonly reported to be isolated and to host distinctive taxa like “Choco.” However, five of 45 biogeographic units were biotically homogenous relative to several other units. These units were “Cuba,” “Chaco,” “Varzea,” “Cauca” and “Costa Pacífica Mexicana.” Also, beta diversity within units was often lower than beta diversity between units at relatively short geographic distances.

Main conclusions

The distribution of Sapotaceae species showed generally low biotic homogeneity within Morrone's (2001, Biogeografia de America Latina y el Caribe. Zaragoza, Spain: CYTED, ORCYT‐UNESCO, Sociedad Entomológica Aragonesa (SEA)) biogeographic units and did not support his biogeographic regionalization. This result suggests a strong role for dispersal and biotic interchange among biogeographic units and across barriers like the Andes. It also casts doubt on the usefulness of Morrone's (2001, Biogeografia de America Latina y el Caribe. Zaragoza, Spain: CYTED, ORCYT‐UNESCO, Sociedad Entomológica Aragonesa (SEA)) biogeographic units as tools for the identification of priority areas for the conservation of biodiversity. However, relatively high biotic homogeneity within some biogeographic units suggests that they capture significant spatial patterns. In particular, noteworthy biotic homogeneity within “Cuba,” “Cauca” and “Costa Pacifica Mexicana” could be explained by isolation. Also, in “Costa Pacifica Mexicana,” patterns of biotic homogeneity could reflect closer affinities to humid lowland montane forest in Central America than to lowland rain forest in South America. Finally, substantial biotic homogeneity within “Varzea” could result from common adaptation to edaphic environments near the Amazon River.

     

New insight into the phylogenetic and biogeographic history of genus Ficus: Vicariance played a relatively minor role compared with ecological opportunity and dispersal

Studies on the evolution of tropical taxa emphasize the role ofvicariance and the break-up of Gondwana in explaining modern distributions.Earlier studies on figs (Ficus spp.) support this view.In the current study,we used an expanded sample (208 spp.) and improved molecular dating techniques to reconstruct the phylogenetic and biogeographic history of Ficus.Consistent with previous studies,our biogeographic analysis indicated that the ancestor of Ficus was present in Gondwana.However,a relaxed clock analysis relying on uncorrelated rates in BEAST suggested that the Neotropical section Pharmacosycea split-off in South America 86.67 Mya,and that other Ficus lineage ancestors originated in India.Most of the basal lineages appeared to have diverged following KT extinction,then rapidly diversified after India collided with continental Asia.The Afrotropical species most likely evolved initially in the Indian subcontinent then dispersed to Africa,either in the late Cretaceous of Madagascar or even later,following the Eocene collision of India with Asia.The Neotropical section Americana,either islandhopped to South America or took a northern route to the Americas through Europe prior to the terminal Eocene global cooling event.Ficus may have arrived in eastern Malesia following the collision of India with Asia,then widely dispersed thereafter.Given the wide ranges in our date estimates,several other scenarios are possible.However,contrary to earlier reports,our analyses suggest that vicariance played a relatively minor role compared with ecological opportunity and dispersal in the diversification of genus Ficus.     

滇东南丫蕊花属(百合科)一新种及其生物地理学意义

报道了云南东南部金平县五台山丫蕊花属(百合科)一新种,并讨论了其生物地理学意义     

One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae: Leptotyphlops sylvicolus Broadley & Wallach, 1997)

We investigate the phylogeographic structure of a fossorial forest‐living snake species, the forest thread snake, Leptotyphlopssylvicolus Broadley & Wallach, 1997 by sampling specimens from the Eastern Cape and KwaZulu‐Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial sequence data (cyt b and ND4), along with population genetic analyses suggest the presence of phylogeographic breaks broadly congruent to those exhibited by other forest‐living taxa. Divergence‐time estimates indicate that cladogenesis within the study taxon occurred during the late Miocene climatic shifts, suggesting that cladogenesis was driven by habitat fragmentation. We further investigate the species‐level divergence within L. sylvicolus by including two partial nuclear loci (PRLR and RAG1). The three species delimitation methods (ABGD, bGMYC, and STACEY), retrieved 10–12 putative species nested within the L. sylvicolus species complex. These results were corroborated by iBPP implementing molecular and morphological data in an integrative Bayesian framework. The morphological analyses exhibit large overlap among putative species but indicate differences between grassland and forest species. Due to the narrow distributions of these putative species, the results of the present study have further implications for the conservation status of the L. sylvicolus species complex and suggest that forest and grassland habitats along the east coast of South Africa may harbor significantly higher levels of diversity than currently recognized.     

Model for the potential natural vegetation mapping of Friuli Venezia-Giulia (NE Italy) and its application for a biogeographic classification of the region

ABSTRACT

The aim of this paper is to present a joint vegetation data base and GIS application to produce a model to map the potential natural vegetation (PNV) of the Friuli-Venezia Giulia region (NE Italy) and to show how the map can be used to draw a biogeographic classification of the region. All the natural arboreal coenoses growing below the timber line, as well as the dwarf shrubs and prairies developing above this limit, were considered. Some cross sections, extracted from the potential vegetation map, were tested against transects of real vegetation distribution.