Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage.

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.

Isolation by resistance explains genetic diversity in the Arremon brushfinches of northern Mesoamerica.

Genetic differentiation between and within natural populations is the result of the joint effects of neutral and adaptative processes. In addition, the spatial arrangement of the landscape promotes connectivity or creates barriers to gene flow, directly affecting speciation processes. In this study, we carried out a landscape genomics analysis using NextRAD data from a montane forest specialist bird complex, the Mesoamerican Chestnut-capped/Green-striped Brushfinch of the genus Arremon. Specifically, we examined population genomic structure using different assignment methods and genomic differentiation and diversity, and we tested alternative genetic isolation hypotheses at the individual level (e.g., isolation by barrier, IBB; isolation by environment, IBE; isolation by resistance, IBR). We found well-delimited genomic structuring (K = 5) across Mesoamerican montane forests in the studied group. Individual-level genetic distances among major montane ranges were mainly explained by IBR hypotheses in this sedentary Neotropical taxon. Our results uncover genetic distances/differentiation and patterns of gene flow in allopatric species that support the role of tropical mountains as spatial landscape drivers of biodiversity. IBR clearly supports a pattern of conserved niche-tracking of suitable habitat conditions and topographic complexity throughout glacial-interglacial dynamics.

The tangled evolutionary history of a long-debated Mesoamerican taxon: The Velazquez Woodpecker (Melanerpes santacruzi, Aves: Picidae).

The Velazquez Woodpecker Melanerpes santacruzi is a highly polytypic species distributed from east-central Mexico to northern Nicaragua. The ample variation in body size, barring of the plumage, and the coloration of nasal tufts, neck, and belly have fueled debates about the taxonomy and evolutionary history of the species; however, the processes generating these patterns of variation and the underlying population dynamics throughout the species' distribution remain poorly understood. Here, we employed reduced representation genome sequencing (NextRAD) and Ecological Niche Modeling methods to test the distinctiveness of the Velazquez Woodpecker based on this new set of genomic data and analyze the correspondence of the genetic structure and ecological differentiation with phenotypic variation and geographic distribution. From phylogenetic and demographic analyses including the Golden-Fronted (M. aurifrons) and Red-bellied Woodpecker (M. carolinus), we obtained results congruent with previous molecular phylogenies. The clades of M. santacruzi and M. carolinus-M. aurifrons are reciprocally monophyletic, although the sister group relationship of M. aurifrons is ambiguous. Using genetic and ecological analyses, we found that the species is structured into three genetically and ecologically differentiated groups comprising the subspecies (1) M. s. santacruzi, (2) M. s. dubius and (3) M. s. grateloupensis-polygrammus-veraecrucis. These groups diverged recently, with two splits between 250,000 and 150,000 years ago, and show a significant genetic admixture among them, especially in their current contact zones. Ecological and demographic models suggest the existence of intermittent areas of sympatry and connectivity among populations of M. santacruzi since the Last Interglacial period. We also found evidence of bi-directional gene flow between the species M. aurifrons and the nearby populations of M. santacruzi (M. s. grateloupensis), along the Sierra Madre Oriental in northeastern Mexico. Gene flow seems to be uneven, with prevalence of movement in the direction from M. aurifrons to M. s. grateloupensis.

Bird Tissues from Museum Collections Are Reliable for Assessing Avian Haemosporidian Diversity.

Birds harbor a diverse group of haemosporidian parasites that reproduce and develop in the host blood cells, muscle tissue, and various organs, which can cause negative effects on the survival and reproduction of their avian hosts. Characterization of the diversity, distribution, host specificity, prevalence patterns, and phylogenetic relationships of these parasites is critical to the study of avian host-parasite ecology and evolution and for understanding and preventing epidemics in wild bird populations. Here, we tested whether muscle and liver samples collected as part of standard ornithological museum expeditions can be examined to study the diversity and distributions of haemosporidians in the same way as blood collected from individual birds that are typically banded and released. We used a standard molecular diagnostic screening method for mitochondrial DNA (cytochrome b) of the parasites and found that blood, muscle, and liver collected from the same host individual provide similar estimates of prevalence and diversity of haemosporidians from the genera Parahaemoproteus and Leucocytozoon. Although we found higher prevalence for the genus Plasmodium when we screened blood vs. liver and muscle samples, the estimates of the diversity of Plasmodium from different tissue types are not affected at the community level. Given these results, we conclude that for several reasons existing museum genetic resources collections are valuable data sources for the study of haemosporidians. First, ornithological museum collections around the world house tens of thousands of vouchered tissue samples collected from remote regions of the world. Second, the host specimens are vouchered and thus host identification and phenotype are permanently documented in databased archives with a diversity of associated ancillary data. Thus, not only can identifications be confirmed but also a diversity of morphological measurements and data can be measured and accessed for these host specimens in perpetuity.

Body mass as a supertrait linked to abundance and behavioral dominance in hummingbirds: A phylogenetic approach.

Body mass has been considered one of the most critical organismal traits, and its role in many ecological processes has been widely studied. In hummingbirds, body mass has been linked to ecological features such as foraging performance, metabolic rates, and cost of flying, among others. We used an evolutionary approach to test whether body mass is a good predictor of two of the main ecological features of hummingbirds: their abundances and behavioral dominance. To determine whether a species was abundant and/or behaviorally dominant, we used information from the literature on 249 hummingbird species. For abundance, we classified a species as "plentiful" if it was described as the most abundant species in at least part of its geographic distribution, while we deemed a species to be "behaviorally dominant" when it was described as pugnacious (notably aggressive). We found that plentiful hummingbird species had intermediate body masses and were more phylogenetically related to each other than expected by chance. Conversely, behaviorally dominant species tended to have larger body masses and showed a random pattern of distribution in the phylogeny. Additionally, small-bodied hummingbird species were not considered plentiful by our definition and did not exhibit behavioral dominance. These results suggest a link between body mass, abundance, and behavioral dominance in hummingbirds. Our findings indicate the existence of a body mass range associated with the capacity of hummingbird species to be plentiful, behaviorally dominant, or to show both traits. The mechanisms behind these relationships are still unclear; however, our results provide support for the hypothesis that body mass is a supertrait that explains abundance and behavioral dominance in hummingbirds.

The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico.

BACKGROUND: Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. RESULTS: We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. CONCLUSIONS: Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetesalbinucha (Aves, Passerellidae).

The White-naped Brushfinch (Atlapetesalbinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A.albinucha and A.gutturalis), but they are presently considered as one polytypic species. Previous studies in the genus Atlapetes have shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography of A.albinucha was analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations of A.albinucha in spite of the species' ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.

Complex biogeographic scenarios revealed in the diversification of the largest woodpecker radiation in the New World.

Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions. Tree topologies from the concatenated and species-tree analyses of the mtDNA and nDNA showed broadly similar patterns, with three relatively well-supported groups apparent: (a) the Sphyrapicus clade (four species); (b) the typical Melanerpes clade, which includes temperate and subtropical dry forest black-backed species; and (c) the mostly barred-backed species, here referred to as the "Centurus" clade. The phylogenetic position of Melanerpes superciliaris regarding the rest of Melanerpes is ambiguous as it is recovered as sister to the rest of Melanerpes or as sister to a group including Sphyrapicus+Melanerpes. Our species tree estimations recovered the same well-delimited highly-supported clades. Geographic range evolution (estimated in BioGeoBEARS) was best explained by a DIVALIKE+j model, which includes vicariance, founder effect speciation, and anagenetic dispersal (range expansion) as important processes involved in the diversification of the largest radiation of woodpeckers in the New World.

Genetic differentiation in the Mexican endemic Rufous-backed Robin, Turdus rufopalliatus (Passeriformes: Turdidae).

The Rufous-backed Robin (Turdus rufopalliatus) is endemic to deciduous and semideciduous tropical forests of western Mexico. Of the currently recognized subspecies, T. r. graysoni, from the Tres Marías Islands and nearby coastal Nayarit, has been considered a separate species; however, this treatment has been challenged due to an apparent contact zone on the mainland, although no hybrids have ever been recorded. Here, we use mitochondrial DNA sequences from individuals sampled across the species' range to assess their phylogeographic relationships. We found reciprocal monophyly between Tres Marías Islands and mainland populations, which share no haplotypes between them. Evolutionary divergence detected within T. rufopalliatus suggests that mainland and island populations have been isolated from each other, and divergence decreases if insular populations are excluded. Demographic parameters suggest that populations are in the process of a rapid expansion from ancestral populations with a lower population size. These results are consistent with morphometric and plumage differences that have been used to recognize the Tres Marías Islands populations from the mainland ones, thus suggesting species status of the island form.

Climate-driven diversification and Pleistocene refugia in Philippine birds: evidence from phylogeographic structure and paleoenvironmental niche modeling.

Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current-day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers. We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep-water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long-term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate-induced refugia acted in concert to produce great species diversity and endemism in the Philippines.

Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae).

The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.

Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura).

Islands have long-attracted scientists because of their relatively simple biotas and stark geographic boundaries. However, for many islands and archipelagos, this simplicity may be overstated because of methodological and conceptual limitations when these biotas were described. One archipelago that has received relatively little recent attention is the Philippine islands. Although much of its biota was documented long ago, taxonomic revision and evolutionary study has been surprisingly scarce, and only a few molecular phylogenetic studies are beginning to appear. We present a molecular phylogeny and taxonomic revision for the Philippine fantails (Aves: Rhipidura) using nuclear and mitochondrial DNA sequences. Our results suggest that current taxonomy underestimates diversity in the group. Some morphologically distinct subspecies warrant species status, whereas one was indistinguishable genetically and morphologically and should not be retained. A few taxa require additional sampling for thorough taxonomic assessment. Patterns of diversity within Philippine Rhipidura mostly corroborate predictions of the Pleistocene aggregate island complex (PAIC) hypothesis, in which diversity is expected to be partitioned by deep water channels separating Pleistocene aggregate islands rather than by current islands. Substantial structure within PAIC clades indicates that additional drivers of diversification should be considered.

Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico.

Cloud forests are distributed in the Neotropics, from northern Mexico to Argentina, under very specific ecological conditions, namely slopes with high humidity input from clouds and mist. Its distribution in Mesoamerica is highly fragmented, similar to an archipelago, and taxa are thus frequently represented as sets of isolated populations, each restricted to particular mountain ranges and often showing a high degree of divergence, both morphologically and genetically. The common bush-tanager (Chlorospingus ophthalmicus, Aves: Thraupidae) inhabits cloud forests from eastern and southern Mexico south to northwestern Argentina. Here we use 676bp of mtDNA (around the ATPase 8 gene) to explore the genetic variation and phylogeographic structure of the Mexican populations of C. ophthalmicus. Phylogenetic analyses of mtDNA sequences indicate deep genetic structure. Five major clades, which segregate according to geographic breaks, are identified (starting from the deepest one in the phylogeny): (1) Southern Chiapas and Northern Central America, (2) Tuxtlas massif, (3) Sierra Madre del Sur, (4) Eastern Oaxaca and Northern Chiapas, and (5) Sierra Madre Oriental. The long history of isolation undergone by each clade, as suggested by the phylogeny, implies that the species status of each of them should be revised.