Ephemeral Pleistocene woodlands connect the dots for highland rattlesnakes of the Crotalus intermedius group

Aim To test how Pleistocene climatic changes affected diversification of the Crotalus intermedius species complex. Location Highlands of Mexico and the south‐western United States (Arizona). Methods We synthesize the matrilineal genealogy based on 2406 base pairs of mitochondrial DNA sequences, fossil‐calibrated molecular dating, reconstruction of ancestral geographic ranges, and climate‐based modelling of species distributions to evaluate the history of female dispersion. Results The presently fragmented distribution of the C. intermedius group is the result of both Neogene vicariance and Pleistocene pine–oak habitat fragmentation. Most lineages appear to have a Quaternary origin. The Sierra Madre del Sur and northern Sierra Madre Oriental are likely to have been colonized during this time. Species distribution models for the Last Glacial Maximum predict expansions of suitable habitat for taxa in the southern Sierra Madre Occidental and northern Sierra Madre Oriental. Main conclusions Lineage diversification in the C. intermedius group is a consequence of Pleistocene climate cycling. Distribution models for two sister taxa in the northern and southern Sierra Madre Occidental and northern Sierra Madre Oriental during the Last Glacial Maximum provide evidence for the expansion of pine–oak habitat across the Central Mexican Plateau. Downward displacement and subsequent expansions of highland vegetation across Mexico during cooler glacial cycles may have allowed dispersal between highlands, which resulted in contact between previously isolated taxa and the colonization of new habitats.     

Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard

The evolutionary history of the Mexican sierras has been shaped by various geological and climatic events over the past several million years. The relative impacts of these historical events on diversification in highland taxa, however, remain largely uncertain owing to a paucity of studies on broadly‐distributed montane species. We investigated the origins of genetic diversification in widely‐distributed endemic alligator lizards in the genus Barisia to help develop a better understanding of the complex processes structuring biological diversity in the Mexican highlands. We estimated lineage divergence dates and the diversification rate from mitochondrial DNA sequences, and combined divergence dates with reconstructions of ancestral geographical ranges to track lineage diversification across geography through time. Based on our results, we inferred ten geographically structured, well supported mitochondrial lineages within Barisia. Diversification of a widely‐distributed ancestor appears tied to the formation of the Trans‐Mexican Volcanic Belt across central Mexico during the Miocene and Pliocene. The formation of filter barriers such as major river drainages may have later subdivided lineages. The results of the present study provide additional support for the increasing number of studies that suggest Neogene events heavily impacted genetic diversification in widespread montane taxa. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 382–394.     

Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships,species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp . ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp , whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets , warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.     

Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico

Neogene vicariance during the Miocene and Pliocene and Quaternary climate change have synergistically driven diversification in Mexican highland taxa. We investigated the impacts of these processes on genetic diversification in the widely distributed bunchgrass lizards in the Sceloporus scalaris group. We searched for correlations between timing in diversification and timing of (1) a period of marked volcanism across the Trans-Mexican Volcanic Belt in central Mexico 3-7.5 million years ago (Ma) and (2) a transition to larger glacial-interglacial cycles during the mid-Pleistocene. From our phylogenetic analyses of mitochondrial DNA we identified two major clades that contained 13 strongly supported lineages. One clade contained lineages from the two northern sierras of Mexico, and the other clade included lineages associated with the Trans-Mexican Volcanic Belt and Central Mexican Plateau. Results provided support for Neogene divergences within the S. scalaris group in response to uplift of the Trans-Mexican Volcanic Belt, a pattern observed in several co-distributed taxa, and suggested that Quaternary climate change likely had little effect on diversification between lineages. Uplift of the Trans-Mexican Volcanic Belt during specific time periods appears to have strongly impacted diversification in Mexican highland taxa.     

Congruent phylogeographic patterns in a young radiation of live‐bearing marine snakes: Pleistocene vicariance and the conservation implications of cryptic genetic diversity

Aim

To investigate phylogeographic patterns among and within co‐occurring sea snake species from Australia's endemic viviparous Aipysurus lineage, which includes critically endangered species, and evaluate the conservation implications of geographically structured patterns of genetic divergence and diversity.

Location

Australia's tropical shallow water marine environments spanning four regions: Great Barrier Reef (GBR), Gulf of Carpentaria (GoC), Timor Sea (TS) and coastal WA (WAC).

Methods

Samples from >550 snakes representing all nine nominal Aipysurus group species were obtained from throughout their known Australian ranges. Coalescent phylogenetic analyses and Bayesian molecular dating of mitochondrial DNA, combined with Bayesian and traditional population genetic analyses of 11 microsatellite loci, were used to evaluate genetic divergence and diversity.

Results

Mitochondrial DNA revealed highly congruent phylogeographic breaks among co‐occurring species, largely supported by nuclear microsatellites. For each species, each region was characterized by a unique suite of haplotypes (phylogroups). Divergences between the TS, GoC and/or GBR were invariably shallow and dated as occurring 50,000–130,000 years ago, coinciding with the cyclic Pleistocene emergence of the Torres Strait land bridge. By contrast, sea snakes from coastal WA were consistently highly divergent from other regions and dated as diverging 178,000–526,000 years ago, which was not associated with any known vicariant events.

Main Conclusions

Previously unappreciated highly divergent sea snake lineages in coastal WA potentially represent cryptic species, highlighting this region as a high‐priority area for conservation. The cyclic emergence of the Torres Strait land bridge is consisted with observed divergences between the TS, GoC and/or GBR; however, processes involved in the earlier divergences involving the WAC remain to be determined. The observed strong population genetic structures (as surrogates for dispersal) indicate that sea snakes have limited potential to reverse population declines via replenishment from other sources over time frames relevant to conservation.

     

Traditional ecological knowledge and use of vegetation in southeastern Mexico: a case study from Solferino, Quintana Roo

In order to assess traditional ecological knowledge of the Maya people in southeastern Mexico, we interviewed local people in Quintana Roo and estimated a number of vegetation variables in two different types of forest which are currently locally exploited, namely Monte alto (medium statured forest) and Sakal che' (low forest). We employed the Use Value index for each plant species (UV_s) to quantify the importance of each plant for each inhabitant. The results showed that this Maya community classify the different forest types by species associations and size, and according to soil appearance. A total of nine categories of use were defined for three plant forms (tree, palm and vine). Manilkara zapota (zapote), Thrinax radiata (chiit) and Macfadyena uncata (bilin kok) showed the highest use values for each plant form. The most common uses were construction (35.5%), medicine (19.0%), craft (17.9%) and edibility (10.3%). There was a weak relationship between the cultural importance of plant species, expressed by the UV_s, and their availability in the medium statured forest and the medium statured–low forest transition expressed by the Importance Value index (IVI). The medium statured forest was the most used forest type, as it provides many species for construction due to external demands rather than to local needs.     

Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae)

Phylogeographical and population genetics methods are used to reconstruct the diversification history of two species of the genus Xiphorhynchus (Aves: Dendrocolaptidae) associated with seasonally flooded forest types in Amazonia. Sequences of the mitochondrial gene cytochrome b were assessed for 21 and 30 individuals, belonging to eight and ten populations, of Xiphorhynchus kienerii and Xiphorhynchus obsoletus , respectively. Uncorrected genetic distances among unique haplotypes recovered ranged only from 0.01% to 0.4% for both species. Over 90% of the genetic variation detected in both species was partitioned within populations, and therefore was not structured geographically. Mismatch distributions and values of Tajima's D -tests indicate that both X. kienerii and X. obsoletus have had small evolutionary effective population sizes, but experienced a recent demographic expansion. These demographic expansions are tentatively dated as occurring over the last 18 000 years BP, a time frame which coincides with the establishment of the early and mid-Holocene age floodplain forest in most of central and eastern Amazonia, following a period of increased river stages throughout the basin. Based on phylogenetic, phylogeographical, and populations genetics data obtained for X. kienerii and X. obsoletus , an evolutionary scenario is proposed to account for the historical diversification of floodplain specialist species in Amazonia.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 383–395.     

An evaluation of new parsimony‐based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony‐based approaches. Here, we compare a parametric method, dispersal–extinction–cladogenesis (DEC), against a parsimony‐based method, dispersal–vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes‐DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World‐wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes‐DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes‐DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events – which in Bayes‐DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes‐DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide‐spanning spatial and temporal model proposed here could prove useful for testing large‐scale biogeographical patterns in plants.     

The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.     

Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa

Aim To investigate the phylogeographical structure of the Guinea multimammate mouse, Mastomys erythroleucus (Temminck, 1853), a widespread murid rodent in sub‐Saharan (Sahel and Sudan) savannas, for a better understanding of the impacts of geographical and historical factors on the evolutionary history of this species, in the context of the growing database of phylogeographical studies of African savanna mammal species. Location Sahel and Sudan savannas, Africa. Methods We sequenced the whole cytochrome b gene in 211 individuals from 59 localities distributed from Senegal to Ethiopia. Sequence data were analysed using both phylogenetic (several rooted tree‐construction methods, median‐joining networks) and population genetic methods (spatial analyses of molecular variance, mismatch distributions). Results Haplotypes were distributed into four major monophyletic groups corresponding to distinct geographical regions across a west–east axis. Diversification events were estimated to have occurred between 1.16 and 0.18 Ma. Main conclusions Vicariance events related to the fragmentation of savanna habitats during the Pleistocene era may explain the phylogeographical patterns observed. Genetic structure was consistent with a role of major Sahelian rivers as significant barriers to west–east dispersal. Recent demographic expansions probably occurred during arid phases of the Holocene with the southward expansion of savannas.     

Freeze-protection of overwintering monarch butterflies in Mexico: critical role of the forest as a blanket and an umbrella

Abstract. 1. At their high-altitude overwintering sites in Mexico, monarch butterflies frequently are subjected to sub-zero°C temperatures during December-March. Although monarchs have moderate supercooling ability, two ecological factors strongly influence their capacity to resist freezing: wetting and exposure to the clear night sky. 2. As shown in Fig. 2, 50% of a population of butterflies with water on their body surfaces freeze at warmer sub-zero temperatures (-4.2°C) compared to butterflies with no water on their bodies (-7.7°C). 100% mortality occurs, respectively, at ?7.7°C and ?15°C. 3. Comparative measurements of rainfall within a large overwintering colony in Mexico indicated that the intact canopy acts as an umbrella that reduces butterfly wetting during winter storms. 4. Variable experimental exposure of butterflies to the clear night sky indicated that openings in the forest canopy increases radiational cooling and causes monarch body temperatures to drop as much as 4°C below ambient air temperature. Monarchs under dense cover had body temperatures approximately the same as the ambient air temperature, but more exposed individuals had body temperatures below ambient in direct proportion to the degree of exposure. Consequently, forest thinning increases the probability that the butterflies will freeze to death. 5. Whereas both wetting and exposure are increased by disturbance of the forest canopy, the interaction of these two factors exacerbates freezing mortality during winter storms: 50% of dry and unexposed butterflies froze at ?8°C, whereas wetted and fully exposed butterflies froze at only ?0.5°C. 6. Butterflies inside and on the bottom of the fir bough clusters are better protected from wetting than those on the outside. This supports the hypothesis that the structure of the butterfly clusters has evolved through individual selection to avoid wetting. 7. The data strongly reinforce previous evidence that forest thinning should be totally prevented within and adjacent to the overwintering sites in order to minimize both wetting and exposure of the butterflies that synergistically increase winter mortality at the overwintering sites in Mexico.     

The Latent Dirichlet Allocation model with covariates (LDAcov): A case study on the effect of fire on species composition in Amazonian forests

Understanding and predicting the effect of global change phenomena on biodiversity is challenging given that biodiversity data are highly multivariate, containing information from tens to hundreds of species in any given location and time. The Latent Dirichlet Allocation (LDA) model has been recently proposed to decompose biodiversity data into latent communities. While LDA is a very useful exploratory tool and overcomes several limitations of earlier methods, it has limited inferential and predictive skill given that covariates cannot be included in the model. We introduce a modified LDA model (called LDAcov) which allows the incorporation of covariates, enabling inference on the drivers of change of latent communities, spatial interpolation of results, and prediction based on future environmental change scenarios. We show with simulated data that our approach to fitting LDAcov is able to estimate well the number of groups and all model parameters. We illustrate LDAcov using data from two experimental studies on the long‐term effects of fire on southeastern Amazonian forests in Brazil. Our results reveal that repeated fires can have a strong impact on plant assemblages, particularly if fuel is allowed to build up between consecutive fires. The effect of fire is exacerbated as distance to the edge of the forest decreases, with small‐sized species and species with thin bark being impacted the most. These results highlight the compounding impacts of multiple fire events and fragmentation, a scenario commonly found across the southern edge of Amazon. We believe that LDAcov will be of wide interest to scientists studying the effect of global change phenomena on biodiversity using high‐dimensional datasets. Thus, we developed the R package LDAcov to enable the straightforward use of this model.     

Influence of the phenolic compound bearing species Ledum palustre on soil N cycling in a boreal hardwood forest

The effects of the understory shrub Ledum palustre on soil N cycling were studied in a hardwood forest of Interior Alaska. This species releases high concentrations of phenolic compounds from green leaves and decomposing litter by rainfall. Organic and mineral soils sampled underneath L. palustre and at nearby non-Ledum sites were amended with L. palustre litter leachates and incubated at controlled conditions. We aimed to know (i) whether L. palustre presence and litter leachate addition changed net N cycling rates in organic and mineral soils, and (ii) what N cycling processes, including gross N mineralization, N immobilization and gross N nitrification, were affected in association with L. palustre. Our results indicate that N transformation rates in the surface organic horizon were not affected by L. palustre presence or leachate addition. However, mineral soils underneath L. palustre as well as soils amended with leachates had significantly higher C/N ratios and microbial respiration rates, and lower net N mineralization and N-to-C mineralization compared to no Ledum and no leachates soils. No nitrification was detected. Plant presence and leachate addition also tended to increase both gross N mineralization and immobilization. These results suggest that soluble C compounds present in L. palustre increased N immobilization in mineral soils when soil biota used them as a C source. Increases in gross N mineralization may have been caused by an enhanced microbial biomass due to C addition. Since both plant presence and leachate addition decreased soil C/N ratio and had similar effects on N transformation rates, our results suggest that litter leachates could be partially responsible for plant presence effects. The lower N availability under L. palustre canopy could exert negative interactions on the establishment and growth of other plant species.