What is the central theme of Jacob Berv’s research?

The central theme is linking microevolutionary processes—genetic change and selection acting within populations—to macroevolutionary patterns across the tree of life. The work integrates genomics, phylogenetics, and paleontology to understand tempo and mode of evolution and the impacts of major Earth history events on diversification.

Which overarching questions guide the research program?

Key questions include: (1) How and why do tempo and mode of evolution vary across genomes and lineages? (2) How have major events in Earth’s history shaped genome evolution and diversification? (3) How can we integrate paleontological and contemporary phylogenetic data to test hypotheses? (4) How can evolutionary regularities ("laws") be used to learn about deep history? (5) How can those regularities inform conservation priorities?

What organisms or systems are typically studied?

The work spans diverse clades across the tree of life, with emphasis on birds as well as projects involving mammals, reptiles, amphibians, fishes, and deep-sea invertebrates. This taxonomic breadth supports comparative inference about evolutionary dynamics.

How are microevolution and macroevolution connected in this research?

Microevolutionary changes in allele frequencies, selection, and demography are modeled and analyzed to understand how they accumulate and interact across timescales to produce macroevolutionary patterns like diversification rate shifts, convergent phenotypes, and trait–environment associations detectable in comparative phylogenetics and the fossil record.

What methods are commonly used to address these questions?

The approach combines molecular phylogenetics, phylogenomic alignment and orthology pipelines, divergence time estimation, ancestral state and rate modeling, macroevolutionary model comparison, and synthesis with paleontological evidence and stratigraphic data. Comparative methods link trait, ecological, and genomic datasets to test explicit evolutionary hypotheses.

How are fossils and paleontological data integrated?

Fossils contribute calibrations for divergence timing, morphological character matrices for total-evidence analyses, and contextual information on extinction, biogeography, and environments through time. Integrating fossil constraints with genomic phylogenies connects deep-time events to modern diversity patterns.

What role do major Earth history events play in the research?

The work examines how mass extinctions and environmental shifts reshape evolutionary trajectories by altering diversification, ecological opportunity, and trait evolution. This includes testing whether lineages exhibit bursts of diversification or rate heterogeneity following global perturbations.

How are rates of evolution estimated and compared across lineages?

Analyses typically fit models of molecular and phenotypic rate variation across phylogenies, compare model fit with information-theoretic criteria, and assess correlations with ecological or life-history covariates. The goal is to identify systematic rate heterogeneity and its drivers.

How does the research evaluate convergence and contingency?

By quantifying repeated evolution of traits and genomic patterns across independent lineages and contrasting those findings with clade-specific contingencies, the work assesses when ecological constraints or opportunities drive similar outcomes versus when historical path-dependence dominates.

Which types of genomic data are analyzed?

Projects may analyze targeted loci, UCEs, exomes, whole genomes, or large gene panels. Data processing includes alignment, orthology inference, site-model testing, and gene-tree/species-tree reconciliation to address discordance and estimate robust phylogenies.

How are phylogenomic conflicts and discordance handled?

Approaches include assessing gene-tree heterogeneity, exploring incomplete lineage sorting versus introgression, and using summary coalescent frameworks and concordance metrics to quantify and interpret conflict across loci.

How are morphological or ecological traits incorporated?

Trait datasets—e.g., skeletal measurements, functional morphology, or ecological niches—are mapped to phylogenies and analyzed with comparative models to test for correlated evolution, adaptive regime shifts, and tempo/mode differences among clades.

How does this work inform biodiversity conservation?

By identifying evolutionary processes and lineages that contribute disproportionately to phylogenetic diversity or exhibit unique evolutionary dynamics, the research provides evidence to prioritize conservation strategies that preserve evolutionary potential and deep-time heritage.

What is the role of fieldwork in the research program?

Fieldwork complements analytical approaches by supporting specimen sampling, ecological and behavioral observations, and environmental metadata collection that improve phylogenetic and comparative analyses across regions such as the Neotropics.

How are biogeographic patterns investigated?

Biogeographic inference leverages time-calibrated phylogenies and distributional data to test historical dispersal, vicariance, and area connectivity hypotheses and to relate geographic dynamics to diversification and trait evolution.

How are methods validated and compared?

Analyses emphasize model adequacy checks, sensitivity analyses to priors and calibrations, replicate datasets, and cross-validation across independent data partitions or alternative methods to ensure robust inference.

What datasets or resources are typically used or produced?

Research outputs may include phylogenetic trees, divergence time estimates, trait matrices, alignment files, and analysis scripts. When possible, data and code are shared via repositories linked on publication pages to facilitate reproducibility.

How does the research approach reproducibility and open science?

Reproducibility is supported through documented workflows, version-controlled code, and public sharing of datasets and analysis scripts associated with publications, enabling independent verification and reuse.

How are software tools and pipelines selected?

Tool choice is driven by the biological question and data scale. The research employs widely used phylogenetic, comparative, and statistical packages, with careful benchmarking and parameter transparency.

What is the value of integrating fossil and modern data?

Integrating fossil evidence anchors timelines and reveals extinct diversity, while modern genomic and ecological data offer resolution and breadth. Together, they enable stronger tests of macroevolutionary hypotheses.

How are uncertainty and model choice communicated?

Analyses report credible intervals, confidence ranges, and alternative model fits, and interpret results with attention to data limitations, calibration uncertainty, and sensitivity to assumptions.

What training or mentoring activities connect to the research?

The program intersects with teaching and mentoring in evolutionary biology, phylogenetics, and data analysis, emphasizing best practices in reproducible research and clear scientific communication.

How do collaborations fit into the research model?

Collaborations across institutions and disciplines contribute diverse expertise—from field biology to paleontology and computational methods—expanding data coverage and enabling integrative analyses.

What types of outputs can readers explore on the site?

Visitors can explore research overviews, news items, and peer-reviewed publications. Publication pages often include citations, links to journal versions, and where available, code and data resources.

How are results contextualized with prior literature?

Results are interpreted alongside the existing literature on diversification, trait evolution, and comparative methods, with an emphasis on how new analyses refine or challenge current understanding.

What is meant by evolutionary tempo and mode?

Tempo refers to the speed of evolutionary change (e.g., substitution or trait rates); mode refers to the processes and patterns (e.g., gradualism, punctuated change, adaptive radiation, convergence). The research quantifies both in a comparative framework.

Why analyze multiple clades rather than focus on one model system?

Comparisons across disparate lineages reveal generalities and exceptions in evolutionary dynamics, increasing the power to detect repeatable patterns and clade-specific contingencies.

How does geography influence evolutionary inference?

Geographic context shapes isolation, dispersal, environmental gradients, and ecological opportunity. Biogeographic models help connect spatial dynamics to rates of trait evolution and diversification.

How is communication of complex results handled for broader audiences?

The site summarizes key findings in accessible language and provides links to detailed publications and data, supporting both specialist and non-specialist readers.

How can students or collaborators engage with the research?

Interested readers can explore publications and news pages for project overviews and contact details. Opportunities vary by project and are typically announced through professional channels and institutional pages.

Where can I find data or code related to published studies?

When public, links to data repositories, code, and supplementary materials are provided on the corresponding publication pages so that others can reproduce and build upon the work.

Research

Jake Berv

Evolutionary Biologist and barbeque enthusiast

A simplified tree of life (evogeneao.com), depicting major events in Earth's history. Major lineages I have studied in published or ongoing research are highlighted in grey.

Field work outside Manaus, Brazil.

Bird survey fieldwork portrait.

Research Focus

I am fascinated by how microevolutionary genetic processes operating at the level of individual organisms and populations propagate through the tree of life and time to generate macroevolutionary patterns. Taking this lens, my research aims to investigate several overarching themes in systematic biology:

What are the roles of evolutionary contingency and convergence in generating patterns of biodiversity?
When and why might one of these modes of evolution predominate over the other?
What are the drivers and correlates of evolutionary change?

Core Questions

Q1How and why do the tempo and mode of evolution vary across genomes and lineages?
Q2How have major events in Earth's history impacted genome evolution and diversification patterns?
Q3How can we integrate paleontological and contemporary phylogenetic data to test hypotheses?
Q4How can evolutionary "laws" be exploited to learn about evolutionary history?
Q5How can evolutionary "laws" inform conservation priorities?

Addressing these questions requires an appeal to both population-scale phenomena, as well as larger-scale patterns that can only be directly observed from the fossil record. This interdisciplinary approach to systematic biology recognizes that variation in the "tempo" (speed) and "mode" (processes) of evolutionary change can confound the interpretation of phylogenetic comparative data.

Below, you can explore branches of my research program, highlighting selected projects across groups of birds, mammals, reptiles, amphibians, fishes, and deep-sea invertebrates.

Research Areas

Phylogeny

Biogeography

Map of Mount Chimborazo in Ecuador. By depicting plant life according to elevation, this map connects disparate climate zones across the globe.

Diversification

Phenotype

Methods & Techniques

Many of my research projects employ a wide variety of techniques that come from different disciplines. You can explore some of these techniques and how I apply them in my work here:

12 families

Phylogenetics 14 papers 10 tags

Time and Rate Inference 15 papers 8 tags

Comparative Modeling 14 papers 10 tags

Population Genomics 8 papers 9 tags

Biogeography 5 papers 5 tags

Diversification 5 papers 5 tags

Model Selection 20 papers 4 tags

Simulation and Validation 11 papers 8 tags

Phenotype and Behavior 10 papers 8 tags

Genomics Infrastructure 3 papers 6 tags

Delimitation 4 papers 4 tags

Integrative Synthesis 14 papers 7 tags

Node size shows how often each method family appears across papers, and edge thickness shows how often two families are used together in the same papers. Click a node or edge to inspect linked papers. For a publication-level pathway view across scale, methods, and themes, see the Interdisciplinarity Braid on the Publications page.