diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
index 8342dbb88..7bfe2a283 100644
--- a/malariagen_data/anopheles.py
+++ b/malariagen_data/anopheles.py
@@ -1,3 +1,4 @@
+import warnings
 from typing import Any, Dict, Mapping, Optional, Tuple, Sequence
 
 import allel  # type: ignore
@@ -444,19 +445,33 @@ def cohort_diversity_stats(
 
         except CacheMiss:
             debug("access allele counts")
-            ac = self.snp_allele_counts(
-                region=region,
-                site_mask=site_mask,
-                site_class=site_class,
-                sample_query=cohort_query,
-                sample_sets=sample_sets,
-                cohort_size=cohort_size,
-                min_cohort_size=min_cohort_size,
-                max_cohort_size=max_cohort_size,
-                random_seed=random_seed,
-                chunks=chunks,
-                inline_array=inline_array,
-            )
+            with warnings.catch_warnings(record=True) as caught_warnings:
+                warnings.simplefilter("always")
+                ac = self.snp_allele_counts(
+                    region=region,
+                    site_mask=site_mask,
+                    site_class=site_class,
+                    sample_query=cohort_query,
+                    sample_sets=sample_sets,
+                    cohort_size=cohort_size,
+                    min_cohort_size=min_cohort_size,
+                    max_cohort_size=max_cohort_size,
+                    random_seed=random_seed,
+                    chunks=chunks,
+                    inline_array=inline_array,
+                )
+            for w in caught_warnings:
+                if "Cohort downsampled" in str(w.message):
+                    msg = str(w.message).split(". Set")[0] + "."
+                    warnings.warn(msg, w.category, stacklevel=2)
+                else:
+                    warnings.warn_explicit(
+                        message=w.message,
+                        category=w.category,
+                        filename=w.filename,
+                        lineno=w.lineno,
+                        source=w.source,
+                    )
 
             debug("compute diversity stats")
             stats = self._block_jackknife_cohort_diversity_stats(