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1. Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

   https://doi.org/10.1111/jbi.13748  

   Marques-Souza, Sergio ; Machado Pellegrino, Katia C. ; Oliveira Brunes, Tuliana ; Carnaval, Ana Carolina ; Pacheco Damasceno, Roberta ; Lima de Oliveira Borges, Manoela ; Candia Gallardo, Carlos ; Rodrigues, Miguel Trefaut ( December 2019 , Journal of Biogeography)

   To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.

   Central Amazonia, Brazil.

   Squamata; Gymnophthalmidae;Loxopholis osvaldoi.

   We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).

   We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.

   Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

    

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2. Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data

   https://doi.org/10.1111/1755-0998.13303  

   Barrow, Lisa N. ; Masiero da Fonseca, Emanuel ; Thompson, Coleen E. P. ; Carstens, Bryan C. ( December 2020 , Molecular Ecology Resources)

   The growing availability of genetic data sets, in combination with machine learning frameworks, offers great potential to answer long‐standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analysed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open‐access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow‐up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this data set, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contained low genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful data sets with greater utility for understanding global biodiversity.

    

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3. Phylogenetic diversity of two geographically overlapping lichens: isolation by distance, environment, or fragmentation?

   https://doi.org/10.1111/jbi.14033  

   Moncada, Bibiana ; Mercado‐Díaz, Joel A. ; Magain, Nicolas ; Hodkinson, Brendan P. ; Smith, Clifford W. ; Bungartz, Frank ; Pérez‐Pérez, Rosa‐Emilia ; Gumboski, Emerson ; Sérusiaux, Emmanuël ; Lumbsch, H. Thorsten ; et al ( January 2021 , Journal of Biogeography)

   Phylogenetic diversification is a precursor to speciation, but the underlying patterns and processes are not well‐studied in lichens. Here we investigate what factors drive diversification in two tropical, morphologically similar macrolichens that occupy a similar range but differ in altitudinal and habitat preferences, testing for isolation by distance (IBD), environment (IBE), and fragmentation (IBF).

   Neotropics, Hawaii, Macaronesia.

   Sticta andina,S. scabrosa(Peltigeraceae).

   We analysed 395 specimens from 135 localities, using the fungal ITS barcoding marker to assess phylogenetic diversification, through maximum likelihood tree reconstruction, TCS haplotype networks, and Tajima's D. Mantel tests were employed to detect structure in genetic vs. geographic, environmental, and fragmentation distances. Habitat preferences were quantitatively assessed by statistical analysis of locality‐based BIOclim variables.

   Sticta andinaexhibited high phenotypic variation and reticulate phylogenetic diversity across its range, whereas the phenotypically uniformS. scabrosacontained two main haplotypes, one unique to Hawaii.Sticta andinais restricted to well‐preserved andine forests and paramos, naturally fragmented habitats due to disruptive topology, whereasS. scabrosathrives in lowland to lower montane zones in exposed or disturbed microsites, representing a continuous habitat.Sticta scabrosashowed IBD only across its full range (separating the Hawaiian population) but not within continental Central and South America, there exhibiting a negative Tajima's D.Sticta andinadid not exhibit IBD but IBE at continental level and IBF in the northern Andes.

   Autecology, particularly preference for either low or high altitudes, indirectly drives phylogenetic diversification. Low diversification in the low altitude species,S. scabrosa, can be attributed to rapid expansion and effective gene flow across a more or less continuous niche due to disturbance tolerance. In contract, high diversification in the high altitude species,S. andina, can be explained by niche differentiation (IBE) and fragmentation (IBF) caused by the Andean uplift.

    

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4. Neo‐sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks ( Eremophila alpestris )

   https://doi.org/10.1111/mec.16357  

   Shakya, Subir B. ; Wang‐Claypool, Cynthia Y. ; Cicero, Carla ; Bowie, Rauri C. K. ; Mason, Nicholas A. ( January 2022 , Molecular Ecology)

   Genetic structure and phenotypic variation among populations are affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low‐elevation desert scrub in Death Valley (285 a.s.l.) to high‐elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD data set of 28,474 SNPs aligned to a high‐quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger‐bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo‐sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo‐sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions—particually on neo‐sex chromosomes—bear stronger associations with the environment.

    

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5. Ecological characteristics explain neutral genetic variation of three coastal sparrow species

   https://doi.org/10.1111/mec.17316  

   Maxwell, Logan M. ; Clark, Jonathan D. ; Walsh, Jennifer ; Conway, Meaghan ; Olsen, Brian J. ; Kovach, Adrienne I. ( March 2024 , Molecular Ecology)

   Eco‐phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species‐specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (N_e) across three closely related and co‐distributed saltmarsh sparrow species differing along a specialization gradient—Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco‐phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity andN_erather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long‐term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist‐generalist status and support the role of an eco‐phylogeographic approach in population and conservation genetics.

    

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