The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.     

Track analysis of the Mexican species of Buprestidae (Coleoptera): testing the complex nature of the Mexican Transition Zone

Aim  We analysed the geographical distributions of species of Buprestidae (Coleoptera) in Mexico by means of a panbiogeographical analysis, in order to identify their main distributional patterns and test the complex nature of the Mexican Transition Zone, located between the Nearctic and Neotropical regions.
Location  Mexico.
Methods  The geographical distributions of 228 species belonging to 33 genera of Buprestidae were analysed. Localities of the buprestid species were represented on maps and their individual tracks were drawn. Based on a comparison of the individual tracks, generalized tracks were detected and mapped. Nodes were identified as the areas where generalized tracks converged.
Results  Thirteen generalized tracks were obtained: one was restricted to the Mexican Transition Zone and five to the Neotropical region (Antillean and Mesoamerican dominions), a further two occurred in both the Nearctic region (Continental Nearctic dominion) and the Mexican Transition Zone, and a further five in both the Neotropical region (Mesoamerican dominion) and the Mexican Transition Zone. Seven nodes were identified at the intersections of the generalized tracks – in the Mesoamerican dominion (Mexican Pacific Coast, Mexican Gulf and Chiapas biogeographical provinces) and the Mexican Transition Zone (Trans-Mexican Volcanic Belt, Balsas Basin and Sierra Madre Oriental biogeographical provinces).
Main conclusions  We conclude that the geographical distribution of Buprestidae is mainly Neotropical, corresponding to the Mesoamerican dominion and the Antillean dominion of the Neotropical region, and the Mexican Transition Zone. Most of the generalized tracks and nodes correspond to the Mexican Transition Zone, thus confirming its complex nature. We suggest that the nodes we have identified could be particularly important areas to choose for conservation prioritization.     

Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid‐late Miocene significantly affected the diversification of the genus in these areas.     

Molecular phylogeny and divergence of major clades in the Puntius complex (Teleostei: Cypriniformes)

Puntius sensu lato (s.l.) was one of the most speciose genera in the family Cyprinidae. There are around 120 valid species widely distributed in South-East and South Asia, and South China. Puntius has long been known as an artificial assemblage and ‘catch-all’ genus in which a large number of small, unrelated cyprinids have been placed. With new species and genera being described each year, obtaining detailed knowledge of the phylogenetic relationships of this complex is critically important in the assessment of a natural classification. In the present study, two mitochondrial and four nuclear genes were used to examine the inter-specific and inter-generic relationships of the Puntius complex and to test the monophyly of the current genera. Divergence time analysis was performed to explore the origin, evolution, and divergence of major clades in Puntius s.l. Results revealed that the genera Puntius seusu stricto (s.s.), Systomus, Pethia, Haludaria, Desmopuntius and Puntigrus were monophyletic with high support. However, monophyly of Barbodes, Striuntius and Sahyadria was not supported. Dawkinsia and Sahyadria formed a highly supported clade. Puntius semifasciolatus and P. snyderi from South China and Taiwan represent a new lineage. Inferences from divergence time analysis indicated that Puntius s.l. likely dated to early Miocene. Major clades in Puntius s.l. diverged during Miocene as well.     

The diversification of Nearctic mammals in the Mexican transition zone

The boundary between the Nearctic and Neotropical regions has been delineated using different approaches, methods and taxa. Using a panbiogeographical approach, identification of nodes can help understand the dynamics and evolution of the boundary. We analysed the distribution patterns of 46 Mexican land mammal species belonging to the Nearctic biotic component and delineated generalized tracks and nodes, in order to determine the southernmost boundary of the Nearctic region in Mexico. We found six generalized tracks and nine nodes; the latter located largely in the Sierra Madre Oriental, Transmexican Volcanic Belt, Sierra Madre del Sur and Chiapas biogeographical provinces. The highlands of Chiapas were found to represent the southernmost area inhabited by Nearctic taxa. The other biogeographical provinces, together with the Sierra Madre Occidental and Balsas Basin provinces, represent the Mexican transition zone in the strict sense. Instead of a classic static boundary, this transition zone represents an evolutionarily 'active' zone, where several speciation events have taken place in the past.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 327–339.     

The scramble for Africa: pan-temperate elements on the African high mountains

The composition of isolated floras has long been thought to be the result of relatively rare long-distance dispersal events. However, it has recently become apparent that the recruitment of lineages may be relatively easy and that many dispersal events from distant but suitable habitats have occurred, even at an infraspecific level. The evolution of the flora on the high mountains of Africa has been attributed to the recruitment of taxa not only from the African lowland flora or the Cape Floristic Region, but also to a large extent from other areas with temperate climates. We used the species rich, pan-temperate genera Carex, Ranunculus and Alchemilla to explore patterns in the number of recruitment events and region of origin. Molecular phylogenetic analyses, parametric bootstrapping and ancestral area optimizations under parsimony indicate that there has been a high number of colonization events of Carex and Ranunculus into Africa, but only two introductions of Alchemilla. Most of the colonization events have been derived from Holarctic ancestors. Backward dispersal out of Africa seems to be extremely rare. Thus, repeated colonization from the Northern Hemisphere in combination with in situ radiation has played an important role in the composition of the flora of African high mountains.     

Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes

The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions of a three-state distribution character (lowland-restricted, lowland-to-highland, highland-restricted), we found that the Andes were colonized twice independently and the tepuis once from lowland-restricted ancestors. Over the entire evolutionary history of Thamnophilus, the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of lowland-restricted distributions. This pattern suggests lowland-restricted distributions are limited not by physiological constraints, but by other forces, such as competition. These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them.     

Molecular evidence for glacial refugia of mountain plants in the European Alps

Many mountain ranges have been strongly glaciated during the Quaternary ice ages, and the locations of glacial refugia of mountain plants have been debated for a long time. A series of detailed molecular studies, investigating intraspecific genetic variation of mountain plants in the European Alps, now allows for a first synopsis. A comparison of the phylogeographic patterns with geological and palaeoenvironmental data demonstrates that glacial refugia were located along the southwestern, southern, eastern and northern border of the Alps. Additional glacial refugia were present in central Alpine areas, where high-elevation plants survived the last glaciation on ice-free mountain tops. The observed intraspecific phylogeographies suggest general patterns of glacial survival, which conform to well-known centres of Alpine species diversity and endemism. This implies that evolutionary or biogeographic processes induced by climatic fluctuations act on gene and species diversity in a similar way.     

A new species of the spider genus Baalzebub (Araneae,Theridiosomatidae) from Brazilian caves

A new species of the spider genus Baalzebub Coddington from Brazil, B. acutum sp. nov., is described and illustrated based on 95 specimens collected from caves around the Iron Quadrangle in the state of Minas Gerais. This species is recognized by male palpal bulb with strong and large conductor covering almost entire embolus, and epigyne of females with long and tapered scape, which extends towards the spinners. Baalzebub acutum sp. nov. is the second species recorded from Brazil, the first for Brazilian caves, bringing the total number of species in the genus to seven in the world.     

The roles of wing color pattern and geography in the evolution of Neotropical Preponini butterflies

Diversification rates and evolutionary trajectories are known to be influenced by phenotypic traits and the geographic history of the landscapes that organisms inhabit. One of the most conspicuous traits in butterflies is their wing color pattern, which has been shown to be important in speciation. The evolution of many taxa in the Neotropics has also been influenced by major geological events. Using a dated, species‐level molecular phylogenetic hypothesis for Preponini, a colorful Neotropical butterfly tribe, we evaluated whether diversification rates were constant or varied through time, and how they were influenced by color pattern evolution and biogeographical events. We found that Preponini originated approximately 28 million years ago and that diversification has increased through time consistent with major periods of Andean uplift. Even though some clades show evolutionarily rapid transitions in coloration, contrary to our expectations, these shifts were not correlated with shifts in diversification. Involvement in mimicry with other butterfly groups might explain the rapid changes in dorsal color patterns in this tribe, but such changes have not increased species diversification in this group. However, we found evidence for an influence of major Miocene and Pliocene geological events on the tribe''s evolution. Preponini apparently originated within South America, and range evolution has since been dynamic, congruent with Andean geologic activity, closure of the Panama Isthmus, and Miocene climate variability.     

Areas of endemism and distribution patterns for Neotropical Piper species (Piperaceae)

Aim The study aimed to establish areas of endemism and distribution patterns for Neotropical species of the genus Piper in the Neotropical and Andean regions by means of parsimony analysis of endemicity (PAE) and track‐compatibility analysis. Location The study area includes the Neotropical region and the Northern Andean region (Páramo‐Punan subregion). Methods We used distribution information from herbarium specimens and recent monographic revisions for 1152 species of Piper from the Neotropics. First, a PAE was attempted in order to delimit the areas of endemism. Second, we performed a track‐compatibility analysis to establish distribution patterns for Neotropical species of Piper. Terminology for grouping Piper is based on recent phylogenetic analyses. Results The PAE yielded 104 small endemic areas for the genus Piper, 80 of which are in the Caribbean, Amazonian and Paranensis subregions of the Neotropical region, and 24 in the Páramo‐Punan subregion of the Andean region. Track‐compatibility analysis revealed 26 generalized tracks, one in the Páramo‐Punan subregion (Andean region), 19 in the Neotropical region, and six connecting the Andean and Neotropical regions. Both the generalized tracks and endemic areas indicate that distribution of Piper species is restricted to forest areas in the Andes, Amazonia, Chocó, Central America, the Guayana Shield and the Brazilian Atlantic coast. Main conclusions Piper should not be considered an Andean‐centred group as it represents two large species components with distributions centred in the Amazonian and Andean regions. Furthermore, areas of greater species richness and/or endemism are restricted to lowland habitats belonging to the Neotropical region. The distribution patterns of Neotropical species of Piper could be explained by recent events in the Neotropical region, as is the case for the track connecting Chocó and Central America, where most of the species rich groups of the genus are found. Two kinds of event could explain the biogeography of a large part of the Piper taxa with Andean–Amazonian distribution: pre‐Andean and post‐Andean events.     

Patterns of Amazonian area relationships based on raw distributions of papilionid butterflies (Lepidoptera: Papilioninae)

Diversifications within a biota are due to several factors. Although some of these are untestable with current analytical methods, hierarchical congruence obtained with different cladistic methods and based on independent taxa are undoubtedly important. In the recent past, most hypotheses of historical biogeography (e.g. refugial, riverine, disturbance, vicariance) were tested on the Amazonian biota, selecting a number of diverse organisms such as plants, anurans, lizards, butterflies, birds and monkeys. In this study we used parsimony analysis of endemicity to infer historical relationships among 16 interfluvial areas in the Amazonian lowlands based on raw distributions of 114 Papilioninae (Lepidoptera). The analysis yielded two most parsimonious trees of area relationships. One tree was characterized by two main clusters of areas which showed a separation of Guyanan + south-east Amazonian interfluvial areas from western Amazonian interfluvial areas. The second tree showed the Guyanan interfluvial areas basal to a cluster which included all the other interfluvial areas. This latter cluster was subdivided into two main groups of areas separating the south-east Amazonian and the western Amazonian interfluvial areas. This result is discussed in the light of previous hypotheses obtained with the same method using some vertebrate taxa in the Amazonian lowlands. Likewise, comparisons with other hypotheses on lineages of birds, mammals and butterflies obtained applying cladistic biogeographical methods are made. The two alternative vicariant patterns presented for papilionid butterflies are strictly congruent with those for birds.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 345–357.     

Biogeographical origins and diversification of the exoneurine allodapine bees of Australia (Hymenoptera,Apidae)

Aim Early diversification of allodapine bees occurred in Africa c. 50 Ma. They are most abundant in sub‐Saharan Africa and Australia, and one of the oldest phylogenetic divergences in the tribe involves a split between an African + Malagasy clade and an Australian clade. The historical biogeographical scenario for this has been highly problematic, entailing an Eocene dispersal from Africa to Australia, followed by an unresolved, and apparently rapid, set of bifurcations leading to the Australian ‘exoneurine’ genera. Here we use an expanded taxon set of Australian species to explore the timing and historical biogeography of the exoneurine radiation. Location Australia, Africa, Madagascar. Methods One nuclear gene (F2 copy of elongation factor 1α) and two mitochondrial genes (cytochrome c oxidase subunit I and cytochrome b) were sequenced for 33 Australian exoneurine species from all five genera found on the continent, as well as for an additional 37 species from all non‐parasitic genera in the remainder of the tribe. We used Bayesian inference analyses to study phylogenetic topology and penalized likelihood analyses to infer key dates of divergence within the tribe. We also used lineage‐through‐time (LTT) analyses and Bayesian analyses to explore the tempo of radiations and biogeographical history of the exoneurines. Results Results from the phylogenetic analyses were congruent with previous studies, indicating a single colonization event c. 34 Ma, too late for Gondwanan vicariance models, and too early for a Laurasian dispersal route. In contrast to earlier studies, we show that this colonization event did not result in an ancient rapid radiation. However, LTT patterns indicated a rapid radiation of the temperate‐adapted genera Exoneura and Brevineura, but not of the xeric‐adapted genus Exoneurella, from 10 to 6 Ma. Main conclusions Our results indicate a trans‐oceanic dispersal event from Africa to Australia, most likely via Antarctica, with an accelerated diversification of temperate‐adapted lineages during the major Late Miocene event referred to as the ‘Hill Gap’. This is the first study to link radiations in Australian bee faunal elements to changing climate, and differs from many other plant and insect phylogenetic studies by showing increased radiation of temperate clades, rather than xeric clades, with increasing aridification of Australia.     

Misconceptions about parsimony analysis of endemicity

Parsimony analysis of endemicity (PAE) has been widely criticized in the recent literature based on methodology rather than on theory. Here I argue that most of the criticisms of PAE result from confusion between the dynamic and static approaches of PAE, by both users and critics of the method. Originally, PAE (the dynamic approach) was proposed primarily for historical comparisons of biotic distributions based on geological and stratigraphical information; that is, the stratigraphical record of the biota within two or more horizons was used to evaluate changes (layer by layer) in their distributional patterns. This led to an analysis of the biota throughout space and through time. On the other hand, the static approach excluded the temporal component and based the analysis on a single geological horizon. Most problems exemplified and discussed in the literature refer to the static approach. In addition to this defence of the original PAE, I present some new criticisms regarding the application of PAE using artificially delimited areas (for example areas defined by geopolitical boundaries), which may lead to incorrect interpretations. Recently, several variations of static PAE have appeared: some designed to accommodate ecological data (e.g. parsimony analysis of distributions – PAD); others that incorporate phylogenetic content (e.g. cladistic analysis of distributions and endemism – CADE); and some that have been integrated with other historical methods (e.g. panbiogeography) in order to detect and evaluate hypotheses of biogeographical homologies. Biogeographers, both ecological and historical, should be aware of the problems and limitations of both dynamic and static PAE and evaluate new variations of PAE (PAD, CADE, etc.). Finally, I argue in favour of an independent and pluralist discipline of biogeography that treats biogeography as related to systematics but not dependent on it, as some scholars have assumed.     

A temporally dynamic approach for cladistic biogeography and the processes underlying the biogeographic patterns of North American deserts

We implemented a temporally dynamic approach to the cladistic biogeographic analysis of 13 areas of North American deserts and several plant and animal taxa. We undertook a parsimony analysis of paralogy‐free subtrees based on 43 phylogenetic hypotheses of arthropod, vertebrate and plant taxa, assigning their nodes to three different time slices based on their estimated minimum ages: Early‐Mid‐Miocene (23?7 Ma), Late Miocene/Pliocene (6.9?2.5 Ma) and Pleistocene (2.4?0.011 Ma). The analyses resulted in three general area cladograms, one for each time slice, showing different area relationships. They allowed us to detect influences of different geological and palaeoclimatological events of the Early‐Mid‐Miocene, Late Miocene/Pliocene and Pleistocene that might have affected the diversification of the desert biota. Several diversification events in the deserts of North America might have been driven by Neogene uplift, marine incursion and the opening of the California Gulf during the Miocene–Pliocene, whereas climatic fluctuations had the highest impact during the Pleistocene.     

Length-weight relationships of fish species from oxbow lakes on the floodplain of the middle Purus River in western Brazilian Amazon

The length-weight relationship (LWRs) was estimated for eight fish species collected from oxbow lakes on the floodplain of the middle Purus River in western Brazilian Amazonia in January, May, and September 2012. The specimens were collected using 12 gillnets (80 m in length × 4 m in height, meshes of between 1.5 cm and 12.0 cm), which were set during both diurnal and nocturnal periods. The species had allometric coefficients (b) of between 2.92 and 3.37, and correlation coefficients (r²) ranging from 0.954 to 0.993 and we highlight that the work presents new data for literature.